HollyArnold 2022-11-08
The Bighorn grant produced roughly three phases of sample events:
“Cross sectional study”: Sheep were brought into basecamp and samples were collected including a single 16S and 18S sample. Diverse metadata was also collected on these sheep (see below for a list of compilation of collected metadata parameters). Following sampling of microbiome, the sheep at basecamp were collared, and their location was followed over time. Field samples were also collected and genetic markers were used to identify how samples mapped to individuals. The samples collected from field samples of bighorn sheep may or may not be collared or have been caputred at basecamp. In order to link these two studies together, a “sample integrity” experiment was carried out where fresh fecal samples were sampled over time if left exposed to the elements.
“Longitudinal study”: Sheep were sampled for a target of 9 times and at each timepoint, microbiome data was collected.
“Parasitic intervention study”: Sheep were captured and the microbiome was measured before and after an antiparasitic medication was given.
This document will describe analysis of the first microbiome samples from the cross sectional study above.
All samples for the sample integrity project, field samples, as well as basecamp samples were processed together to determine ASV content. By processing ASVs together, we will be able to compare any ASVs that of interest between studies. ASVs for the sample integrity project will be split off after determination of ASVs and cladal analysis will not be performed on these now. The remaining two projects (field samples and basecamp samples) were are split into two projects and they will be processed separately to (1) determine if there are samples that should be removed due to low numbers of sequences and (2) determine appropriate rarefaction methods.
Some statistics of the files that we have for the cross sectional analysis. In the event that two extraction steps were performed per sample (i.e. a technical duplicate) the sample with the largest number of sequences was kept for all further analysis. The sample with the lower amount of sequences was excluded from all further analysis.
16S raw fastQ files 446 samples = 892 files Number of duplicated 16S sequences 4 samples = 8 files Number of unique animal IDs 442 samples = 884 files Number of samples post technical filter 442 samples = 884 files
18S raw fastQ files 445 samples = 890 files Number of duplicated 16S sequences 3 samples = 6 files Number of unique animal IDs 442 samples = 884 samples
In order to determine how dada2 parameters impacted unique ASVs of each project, I did a parameter sweep here to determine how trim length impacts the number of unique ASVs retained for each project and overall. Numbers in parenthasis for Basecamp ASVs, Field ASVs and Integrity ASVs columns represent the number of ASVs retained after excluding ASVs that occur <= 5 times.
| FWD_TRIM | REV_TRIM | EE | N_ASVs | Mean (min - max) ASVs Retained | Basecamp ASVs | Field ASVs | Integrity ASVs | Pool |
|---|---|---|---|---|---|---|---|---|
| 250 | 200 | 2,2 | 9943 | 62% (52 - 71) | 9476 (8230) | 9618 (8744) | 8152 (6349) | T |
| 200 | 150 | 2,2 | 40741 | 71% (60 - 83%) | 24900 (9872) | 26992 (10929) | 20318 (7329) | T |
| 225 | 175 | 2,2 | 14007 | 67% (56 - 78) | 11563 (8452) | 11962 (8935) | 9701 (6412) | T |
| 250 | 200 | 0,0 | 0 | 0% (0 - 0) | 0 | 0 | 0 | T |
| 200 | 150 | 0,0 | 0 | 0 (0 - 0) | 0 | 0 | 0 | T |
250 | 200 | 2,2 | 16846 | 70% (64 - 78) | 8124 (5072) | 9323 (8744)|
5211 (2957) | F |
200 | 150 | 2,2 | 12077 | 73% (64 - 83) | 6485 (4760) | 7239 (5379)
|3870 (2649) | F |
225 | 175 | 2,2 | 15601 | 74% (66 - 83) | 7864 (5161) | 8776 (5789)|4831
(2917) | F |
“Universal” 16S sequencing primers were utilized from the Earth Microbiome Project 16S Illumina Amplicon Protocol. Forward (5’-GTGYCAGCMGCCGCGGTAA-3’) and reverse primers (5’-GGACTACNVGGGTWTCTAAT-3’) amplified the V4 hypervariable region.
ASVs were determined using the Divisive Amplicon Denoising ALgorith (DADA2; version 1.22.0) pipeline in R (Bird Hippie; version 4.1.2). A forward primer and reverse reverse-complement primer were trimmed off the forward reads and the the reverse and forward-reverse complement were trimmed from the reverse reads using cutadapt (version 4.1).
Forward reads were trimmed at 250 basepairs and reverse reads were trimmed at 200 basepairs after examining quality scores and removing reads with any ambiguous bases. Convergent error model parameterization and sample inference was estimated for forward and reverse reads. Paired ends were merged, and chimeras were excluded.
The following quality plots show the overall statistics for all samples of the cross sectional analysis considered.
A note for those reading this document on the GitLab page: Please see
README.pdf for these following plots as they don’t render correctly on
GitLab, but they do on the PDF file. These are ugly plots that are
automatically generated. Note that you can make your own plots from data
that look prettier if desired from
data/dada2_processing/bighorn_2023-02-07_output_dada2Run.RData.
rsync -avz /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep/dada2.out/16S/bighorn_2023-02-07_output/ /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep/population_structure_of_the_immunomicrobiome/data/dada2_processing/
cp params16S.txt /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep/population_structure_of_the_immunomicrobiome/data/dada2_processing/The forward error rates:
The reverse error rates:
Collector’s curves:
Heatmap of numbers of sequences kept at each step. Most are removed during quality filtering after cutting off primers.
The read depth distribution of all samples
The read length distribution of all samples. As expected most ASVs are of similar length. There are some longer than expected ASVs that might have merged incorrectly or are likely eukaryotic contamination that should be filtered out by the user before proceeding with ASVs.
Look for the presence of primers present in the first 10 files pre cut. As can be seen there is signifcaint read through of the reverse complement of the forward primer in the reverse reads and the reverse compliment of the reverse primer in the forward reads. This is common since CQLS doesn’t look for the read through of any primers or adapters at the end of reads.
pwd
head -n 70 data/dada2_processing/initialPrimers.txt## /Users/arnoldhk/Desktop/Research/2022_Bighorn_Sheep/population_structure_immunomicrobiome_gitlab
## [1] 1
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s003-index-TGACTAATGGCC-TS032-16S-1-C1_S3_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 7535
## REV.ForwardReads 0 0 0 15976
## REV.ReverseReads 0 0 0 0
## [1] 2
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s004-index-GTGGAGTCTCAT-TS032-16S-1-D1_S4_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 7438
## REV.ForwardReads 0 0 0 17446
## REV.ReverseReads 0 0 0 0
## [1] 3
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s005-index-TGATGTGCTAAG-TS032-16S-1-E1_S5_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 12007
## REV.ForwardReads 0 0 0 27592
## REV.ReverseReads 0 0 0 0
## [1] 4
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s006-index-TGTGCACGCCAT-TS032-16S-1-F1_S6_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 11470
## REV.ForwardReads 0 0 0 25932
## REV.ReverseReads 0 0 0 0
## [1] 5
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s007-index-GGTGAGCAAGCA-TS032-16S-1-G1_S7_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 12999
## REV.ForwardReads 0 0 0 30671
## REV.ReverseReads 0 0 0 0
## [1] 6
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s008-index-CTATGTATTAGT-TS032-16S-1-H1_S8_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 22972
## REV.ForwardReads 0 0 0 50955
## REV.ReverseReads 0 0 0 0
## [1] 7
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s011-index-CGGGACACCCGA-TS032-16S-1-C2_S11_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 6929
## REV.ForwardReads 0 0 0 15887
## REV.ReverseReads 0 0 0 0
## [1] 8
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s012-index-ACCTTACACCTT-TS032-16S-1-D2_S12_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 10104
## REV.ForwardReads 0 0 0 22056
## REV.ReverseReads 0 0 0 0
## [1] 9
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s013-index-GTAGTAGACCAT-TS032-16S-1-E2_S13_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 10273
## REV.ForwardReads 0 0 0 23259
## REV.ReverseReads 0 0 0 0
## [1] 10
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s014-index-CCGGACAAGAAG-TS032-16S-1-F2_S14_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 7589
## REV.ForwardReads 0 0 0 17116
## REV.ReverseReads 0 0 0 0Look for the presence of primers present in the first 10 files post cut. Our cut adapt worked to trim these off!
pwd
head -n 70 data/dada2_processing/cutPrimers.txt## /Users/arnoldhk/Desktop/Research/2022_Bighorn_Sheep/population_structure_immunomicrobiome_gitlab
## [1] 1
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s003-index-TGACTAATGGCC-TS032-16S-1-C1_S3_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 2
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s004-index-GTGGAGTCTCAT-TS032-16S-1-D1_S4_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 3
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s005-index-TGATGTGCTAAG-TS032-16S-1-E1_S5_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 4
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s006-index-TGTGCACGCCAT-TS032-16S-1-F1_S6_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 5
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s007-index-GGTGAGCAAGCA-TS032-16S-1-G1_S7_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 6
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s008-index-CTATGTATTAGT-TS032-16S-1-H1_S8_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 7
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s011-index-CGGGACACCCGA-TS032-16S-1-C2_S11_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 8
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s012-index-ACCTTACACCTT-TS032-16S-1-D2_S12_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 9
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s013-index-GTAGTAGACCAT-TS032-16S-1-E2_S13_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0
## [1] 10
## [1] "/nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s014-index-CCGGACAAGAAG-TS032-16S-1-F2_S14_R1_001.fastq.gz"
## Forward Complement Reverse RevComp
## FWD.ForwardReads 0 0 0 0
## FWD.ReverseReads 0 0 0 0
## REV.ForwardReads 0 0 0 0
## REV.ReverseReads 0 0 0 0Look at the first bit of cut adapt for the first file. As can be seen, most of the sequences trimmed off were around 48 base pairs. All reads passed cutting of primers.
pwd
head -n 270 data/dada2_processing/cutAdaptOutput.txt ## /Users/arnoldhk/Desktop/Research/2022_Bighorn_Sheep/population_structure_immunomicrobiome_gitlab
##
## ### This is cutadapt 2.6 with Python 3.7.12
##
##
## ### Command line parameters: -g GTGYCAGCMGCCGCGGTAA -a ATTAGAWACCCBNGTAGTCC -G GGACTACNVGGGTWTCTAAT -A TTACCGCGGCKGCTGRCAC -n 2 -m 1 -j 100 -e 0.1 -o /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s003-index-TGACTAATGGCC-TS032-16S-1-C1_S3_R1_001.fastq.gz -p /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s003-index-TGACTAATGGCC-TS032-16S-1-C1_S3_R2_001.fastq.gz /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s003-index-TGACTAATGGCC-TS032-16S-1-C1_S3_R1_001.fastq.gz /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s003-index-TGACTAATGGCC-TS032-16S-1-C1_S3_R2_001.fastq.gz
##
##
## ### Processing reads on 100 cores in paired-end mode ...
##
##
## ### Finished in 7.16 s (366 us/read; 0.16 M reads/minute).
##
##
## ###
##
##
## ### === Summary ===
##
##
## ###
##
##
## ### Total read pairs processed: 19,550
##
##
## ### Read 1 with adapter: 18,213 (93.2%)
##
##
## ### Read 2 with adapter: 12,903 (66.0%)
##
##
## ### Pairs that were too short: 0 (0.0%)
##
##
## ### Pairs written (passing filters): 19,550 (100.0%)
##
##
## ###
##
##
## ### Total basepairs processed: 11,768,821 bp
##
##
## ### Read 1: 5,884,550 bp
##
##
## ### Read 2: 5,884,271 bp
##
##
## ### Total written (filtered): 10,273,440 bp (87.3%)
##
##
## ### Read 1: 5,009,542 bp
##
##
## ### Read 2: 5,263,898 bp
##
##
## ###
##
##
## ### === First read: Adapter 1 ===
##
##
## ###
##
##
## ### Sequence: GTGYCAGCMGCCGCGGTAA; Type: regular 5'; Length: 19; Trimmed: 0 times.
##
##
## ###
##
##
## ### === First read: Adapter 2 ===
##
##
## ###
##
##
## ### Sequence: ATTAGAWACCCBNGTAGTCC; Type: regular 3'; Length: 20; Trimmed: 18213 times.
##
##
## ###
##
##
## ### No. of allowed errors:
##
##
## ### 0-9 bp: 0; 10-19 bp: 1
##
##
## ###
##
##
## ### Bases preceding removed adapters:
##
##
## ### A: 0.1%
##
##
## ### C: 0.1%
##
##
## ### G: 99.5%
##
##
## ### T: 0.3%
##
##
## ### none/other: 0.0%
##
##
## ### WARNING:
##
##
## ### The adapter is preceded by "G" extremely often.
##
##
## ### The provided adapter sequence could be incomplete at its 3' end.
##
##
## ###
##
##
## ### Overview of removed sequences
##
##
## ### length count expect max.err error counts
##
##
## ### 3 7 305.5 0 7
##
##
## ### 28 1 0.0 2 1
##
##
## ### 46 2 0.0 2 0 2
##
##
## ### 47 290 0.0 2 226 64
##
##
## ### 48 16503 0.0 2 14604 1899
##
##
## ### 49 1407 0.0 2 1143 264
##
##
## ### 50 3 0.0 2 2 1
##
##
## ###
##
##
## ###
##
##
## ### === Second read: Adapter 3 ===
##
##
## ###
##
##
## ### Sequence: GGACTACNVGGGTWTCTAAT; Type: regular 5'; Length: 20; Trimmed: 0 times.
##
##
## ###
##
##
## ### === Second read: Adapter 4 ===
##
##
## ###
##
##
## ### Sequence: TTACCGCGGCKGCTGRCAC; Type: regular 3'; Length: 19; Trimmed: 13029 times.
##
##
## ###
##
##
## ### No. of allowed errors:
##
##
## ### 0-9 bp: 0; 10-19 bp: 1
##
##
## ###
##
##
## ### Bases preceding removed adapters:
##
##
## ### A: 91.6%
##
##
## ### C: 5.0%
##
##
## ### G: 2.3%
##
##
## ### T: 1.2%
##
##
## ### none/other: 0.0%
##
##
## ### WARNING:
##
##
## ### The adapter is preceded by "A" extremely often.
##
##
## ### The provided adapter sequence could be incomplete at its 3' end.
##
##
## ###
##
##
## ### Overview of removed sequences
##
##
## ### length count expect max.err error counts
##
##
## ### 3 125 305.5 0 125
##
##
## ### 4 1 76.4 0 1
##
##
## ### 9 1 0.1 0 0 1
##
##
## ### 47 163 0.0 1 72 91
##
##
## ### 48 11890 0.0 1 6988 4902
##
##
## ### 49 846 0.0 1 474 372
##
##
## ### 50 3 0.0 1 1 2
##
##
## ###
##
##
## ###
##
##
## ### WARNING:
##
##
## ### One or more of your adapter sequences may be incomplete.
##
##
## ### Please see the detailed output above.
##
##
## ### This is cutadapt 2.6 with Python 3.7.12
##
##
## ### Command line parameters: -g GTGYCAGCMGCCGCGGTAA -a ATTAGAWACCCBNGTAGTCC -G GGACTACNVGGGTWTCTAAT -A TTACCGCGGCKGCTGRCAC -n 2 -m 1 -j 100 -e 0.1 -o /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s004-index-GTGGAGTCTCAT-TS032-16S-1-D1_S4_R1_001.fastq.gz -p /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//cut/lane1-s004-index-GTGGAGTCTCAT-TS032-16S-1-D1_S4_R2_001.fastq.gz /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s004-index-GTGGAGTCTCAT-TS032-16S-1-D1_S4_R1_001.fastq.gz /nfs3/Sharpton_Lab/prod/prod_restructure/projects/arnoldhk/2022_Bighorn_Sheep//raw.tmp.links/raw.tmp.links.16S//filtN/lane1-s004-index-GTGGAGTCTCAT-TS032-16S-1-D1_S4_R2_001.fastq.gz
##
##
## ### Processing reads on 100 cores in paired-end mode ...CDFW_Animal_ID: The California Department of Fish
and Wildlife Animal ID number. This ID number has the following
properties:
Permanent_ID: The permanent ID number for an
individual. Unlike the DEBS/ PEBS number which can change between
seasons, the permanent ID is always the same for each individual
regardless of capture season.
Metapopulation_Name: Describes if the individual was
captured from a population from within the Mojave / Death Valley
(i.e. DEBS) region or the Peninsular (i.e. PEBS) region.
Population: An English tag that is used to describe
populations (as is the case for Mojave populations) or ewe groups (as is
the case for Peninsular groups). The english tag can be thought of a
rough proxy for population structure, though genetic data will be
better.
Capture_Date: Date animal was captured.
Season: Season animal was captured.
Age: Estimated age of animal.
Sex: Animal sex.
Lactating: Lactation presence (1) or absence
(0).
Pregnant: Pregnancy presence confirmed via
ultrasound (1) or absence (0).
UTM_Region: UTM coordinate region.
UTM_Easting: UTM Easting.
UTM_Northing: UTM Northing
World_Geodetic_System: From Wikipedia (https://en.wikipedia.org/wiki/World_Geodetic_System):
“The World Geodetic System (WGS) is a standard used in cartography,
geodesy, and satellite navigation including GPS. The current version,
WGS 84, defines an Earth-centered, Earth-fixed coordinate system and a
geodetic datum, and also describes the associated Earth Gravitational
Model (EGM) and World Magnetic Model (WMM). The standard is published
and maintained by the United States National Geospatial-Intelligence
Agency.” All coordinates were taken with WGS84 for Peninsular and for
Mojave populations.
Time_Capture: Capture time start.
Time_Release: Capture time release.
Catch_Duration: Time animal was in
processing.
Chase_Duration_Seconds: How long the animal was
pursued with the helicopter.
Subjective_Body_Condition: Team subjective body
condition score.
Field_Contagious_Ecthyma: Presence (1) or absence
(0) of Contagious Ecthyma noted on capture.
Field_Sinusitis: Presence (1) or absence (0) of
sinusitis noted during capture.
Field_Coughing: Presence (1) or absence (0) of
coughing noted during capture.
Field_Nasal_Discharge: Presence (1) or absence (0)
of nasal discharge noted during capture.
Field_Notes: Notes from the field team.
Ear_Tag_Right: Right ear tag color and
number.
Ear_Tag_Left: Left ear tag color and
number.
Mojave_Weight_kg: Sheep weight (kg). Available for
Mojave populations only.
Mojave_Relative_Body_Condition_Score: Subjective
body condition scoring in the Mojave sheep on a scale of 5.
Mojave_Teeth_Present: Teeth present notated by the
Modified Triadan System.
Mojave_Tooth_Notes: Field team notes about
teeth.
Mojave_Lifestage: Animal lifestage.
Mojave_Body_Length: Body length (cm) measured from
nose to rump. Available for Mojave only.
Mojave_Chest_Girth_cm: Chest girth (cm). Available
for Mojave only.
Mojave_Metatarsal_Length_cm: Metatarsal length (cm).
Available for Mojave only.
Mojave_Neck_Circumference_Cranial_cm: Neck
circumference (cm) measured just caudal to the mandibular ramus at
approximately C2. Available for Mojave only.
Mojave_Neck_Circumference_Mid_cm: Neck circumference
(cm) measured within the mid cervical region at approximately C4.
Available for Mojave only.
Mojave_Right_Horn_Length_cm: Right horn length (cm).
Available for Mojave animals only.
Mojave_Right_Horn_Diameter_cm: Right horn diameter
(cm). Available for Mojave animals only.
Mojave_Left_Horn_Length_cm: Left horn length (cm).
Available for Mojave animals only.
Mojave_Left_Horn_Diameter_cm: Left horn diameter
(cm). Available for Mojave animals only.
US_Max_Fat_cm: Subcutaneous fat thickness was
measured at its thickest point cranial to the cranial process of the
tuber ischium (pin bone) and 3 cm
from the spine (method is detailed in Stephenson et al 2020). Available
for Mojave animals only.
US_Beta_Femorus_cm: Ultrasound measurement of beta
femorus muscle. Method is detailed in Stephenson et al 2020.
US_Latissimus_Dorsi_cm: Ultrasound measurement of
the latissimus dorsi muscle. Method is detailed in Stephenson et al
2020.
Ingesta_Free_Body_Fat_Percent: Ingesta free body fat
(IFBFat) percent is calculated from ultrasound measurements taken at
caputre. Stephenson 2020 found that IFBFat exhibit strong linear
relationships with in vivo and postmortem indices in bighorn sheep:
13.28*x_1 + 7.78, where x_1 is the max fat pad
measured as described in US_Max_Fat_cm. When the max fat
measurement was equal to zero, then it was calculated with the equation
3.92*x_2 - 1.48, where x_2 is equal to
Mojave_Relative_Body_Condition_Score.Ingestia_Free_Body_Fat_kg: Calculated from line of
best fit for Stephenson et al. 2020. See note in
Ingesta_Free_Body_Fat_Percent. When the max fat measurement
was greater than 0, then IFBFat was calculated with the
equation6.85*x_1 + 3.28, where x_1 is the max
fat pad measured as described in US_Max_Fat_cm. When the
max fat measurement was equal to zero, then it was calculated with the
equation 2.11*x_2 - 1.46, where x_2 is equal
to Mojave_Relative_Body_Condition_Score. Reported
R^2 values respectively were 0.80 and 0.73.
Mojave_Udder_Size: Subjective udder size noted by
the field team.
Mojave_Milk_Expressed: Presence (1) or absence (0)
of animal lactating.
Mojave_Injuries_Noted: Field team notes about
injuries that were noted in the field.
Mojave_Vital_Time_1 -
Mojave_Vital_Time_7: Capture times where vitals are
measured.
Mojave_Temp_1 - Mojave_Temp_7:
Temperatures that were measured at corresponding capture times 1 - 7
above.
Mojave_Resp_1 - Mojave_Resp_7:
Temperatures that were measured at corresponding capture times 1 - 7
above.
Mojave_HR_1 - Mojave_HR_7: Heart rates
that were measured at corresponding capture times 1 - 7 above.
GPS_Collar_Frequency: GPS collar frequency.
GPS_Collar_Serial_Number: GPS collar serial
number.
VHF_Collar_Frequency: VHF collar frequency. VHF
collars transmit a very high frequency compared to GPS collar. They are
used to track the animals in the field to gather data on long term
survival because they can collect data long after the GPS collar
typically dies.
VHF_Collar_Serial_Number: VHF collar serial
number.
GPS_Color: GPS collar color.
VHF_Color: VHF collar color.
GPS_Measurement: GPS collar measurement around the
neck.
VHF_Measurement: VHF collar measurement around the
neck.
GPS_Collar_Notes: Notes from the tech team about how
the collar is fitting.
GPS_Manufacturer: Company manufacturer of collars
used in field.
Mojave_RIT_Bolus_ID: Rumen Implant Transmitters
(RIT) ID number.
Mojave_RIT_Swallowed: RIT swallowed (1) or not
(0).
Mojave_Sample_Blood: Blood sample collected (1) or
missing (0).
Mojave_Pharyngeal_Swab: Pharyngeal swab collected
(1) or missing (0).
Mojave_Sample_Nasal_Swab: Nasal swab collected (1)
or missing (0).
Mojave_Sample_Parasite: Fecal sample collected (1)
or missing for parasite composition analysis.
Mojave_Sample_Ear_Swab: Ear swab collected (1) or
missing (0).
Mojave_Sample_Feces: Fecal sample collected (1) or
missing (0).
Mojave_Sample_Hair: Hair sample collected (1) or
missing (0).
Mojave_Sample_Photo: Photo taken (1) or missing
(0).
Mojave_Medications_Administered: Medications
administered (1) or not (0) during field collection.
Mojave_Prophylaxis_VIT_MuSE: Sheep were administered
(1) or not administered MU-SE on capture. MU-SE (selenium, vitamin E) is
an emulsion of selenium-tocopherol for the prevention and treatment of
(Selenium-Tocopherol Deficiency) syndrome in weanling calves and
breeding beef cattle.
Mojave_Treatments_Administered: Noted if additional
treatments were administered to Mojave sheep during capture.
Mojave_Sample_Collection_Location: Location that
samples were processed. Field means that the helicopter team collected
the samples from the sheep netted down. This often happened if weather
conditions worsened and it was not safe to transport the sheep to
basecamp via helicopter (e.g. wind speed). If sheep were processed in
basecamp, then sheep were transported via helicopter to basecamp and
samples were collected by the team listed. Often times, more samples
will be collected from those sheep that were transported into basecamp
than those sheep that were left in the field.
Mojave_Range_Code: Mojave mountain range code from
the location of capture (see
Mojave_Capture_Location).
Mojave_Range_County: County that the sheep were
captured in.
Mojave_Capture_Location: The caputre
location.
Mojave_Capture_Location_Long: The relative location
that the sheep were captured in that is often reported as a relitive
location that is listed in Mojave_Capture_Location
column.
Mojave_Recorder_Name: The person that recorded data
on each sheep that was captured and processed in basecamp.
Mojave_Capture_Team: Team that was involved in the
capture of the sheep (helicopter team).
Mojave_Sample_Collection_Team: Names of the team
that was involved in collecting the samples that were gathered from the
basecamp sheep.
Mojave_Capture_Method: The method that was employed
by the capture helicopter team. All sheep in the Mojave were captured
via helicopter net gut.
Mojave_Slow_To_Move_Post_Capture: If sheep were
returned to the field and then the helicopter team noticed that they
were slow to move post release, this is indicated as a 1. Most sheep
recorded during this year got up quickly on release.
Pen_Ewe_Group: The ewe group of the Peninsular
region. The Ewe group is a proxy for the population structure of the
populations within the Peninsular region. Note that ewe group in this
region is probably a much rouger proxy for population structure than
that of the Mojave region. The reason for this is that population ranges
tend to be liner and parallel to one another and so it is thought that
there is much mroe crossover between populations in this region. Ewe
group assignments also have much more debate to the assignment of an
individual sheep to the group comparatively to the sheep that are
assigned a population within the Mojave region.
Pen_Recovery_Region: The recovery region short hand
of where the sheep were capture within the Peninsular ranges.
Pen_Recovery_Region_Full: The full name of the
recovery region.
Pen_Recovery_Region_Notes: Notes regarding the
region in which the sheep was captured.
Pen_Lattitude: Lattitude of the GPS location of the
Peninsular sheep.
Pen_Longitude: Longitude of the GPS location of the
Peninsular sheep on capture.
Pen_Temperature: Temperature on capture.
Pen_Field_Behavior: Notes on behavior during capture
in Peninsular region.
Plate_Location: Location of sample during extraction
and sequencing. Contains both Plate_ID and
Well_ID.
Plate_ID: Plate ID number for sequencing.
Well_ID: Well ID number for sequencing.
Sampling_Location: Location that samples were taken
from. “Basecamp” samples were either taken by the helicopter team in the
field, or they were taken by scientists in the basecamp after the
helicopter team transported the sheep. “Field” samples were those
samples that were collected by sheep bedsides. “Longitudinal integrity
samples” were an experiment that was conducted to see how long after
fecal sample production the microbial communities showed
changes.
Barcode_18S: The 18S sample barcode used for
sequencing.
Sharpton_Internal_Project_ID_18S: The internal
Sharpton Lab project ID that is used to map sequencing runs to projects
within the lab.
Raw_FastQ_Server_Location_18S: The location on the
server where raw 18S sequences are stored.
Raw_FastQ_Forward_Name_18S: The fastq file name of
the raw forward 18S reads.
Sequencing_Lane_18S: The sequncing lane that samples
were run in.
Sequencing_ID_18S: The sample ID for the 18S
sequences that was assigned during sequencing.
Raw_FastQ_Reverse_Name_18S: The fastq file name of
the raw reverse 18S reads.
path_tmp_data_18S: A temporary back up copy of the
18S sequences used for analysis.
path_tmp_links_18S: A temporary symbolic link to the
copy of the 18S used for analysis.
Lines_18S: The number of lines in the raw 18S
forward sequencing file.
Barcode_16S: The 16S sample barcode used for
sequencing.
Sharpton_Internal_Project_ID_16S: The internal
Sharpton Lab project ID that is used to map sequencing runs to projects
within the lab.
Raw_FastQ_Server_Location_16S: The location on the
server where raw 16S sequences are stored.
Raw_FastQ_Forward_Name_16S: The fastq file name of
the raw forward 16S reads.
Sequencing_Lane_16S: The sequncing lane that samples
were run in.
Sequencing_ID_16S: The sample ID for the 18S
sequences that was assigned during sequencing.
Raw_FastQ_Reverse_Name_16S: The fastq file name of
the raw reverse 16S reads.
path_tmp_data_16S: A temporary back up copy of the
16S sequences used for analysis.
path_tmp_links_16S: A temporary symbolic link to the
copy of the 16S used for analysis.
Lines_16S: The number of lines in the raw 16S
forward sequencing file.
PCV: Pack cell volume (%). In a paper by Borjesson
et al. 2000, reported reference intervals for PCV in free ranging desert
bighorn sheep for HEMATOCRIT was 44.3% - 56.2% for females and 33.2% -
56.3% for males.
TP: Total protein taken from capillary tube along
with PCV.
Mojave_Death_Date: Death date of an animal. Dates in
the death column are animals that were retrieved upon death.
Mojave_Mortality_Date: Death date of an animal.
Dates in the mortality column are animals that were not retrieved upon
death.
GPS_Collar_End_Date: Date that the GPS signal cut
out in the event the sheep did not die but the collar stopped working.
RIT was used to confirm the date the GPS end date is either when the GPS
collar dropped off, The GPS collar failed (stopped recording). It is
also possible that it is a day or two after the mortality date so that
the temperature / HR data was not truncated too soon.
RIT_End_Date: Date that RIT Collar stopped
recording.
Mortality_Notes: Notes regarding
Mojave_Death_Date, Mojave_Mortality_Date,
GPS_Collar_End_Date, or RIT_End_Date.
VDL_Chemistry_Accession_Number: VDL report accession
number for chemistry values (BUN, Cr, Glucose, Cholesterol,
Triglycerides, TP, Albumin, Globulin, Bilirubin, Calcium, Chloride, CK,
GGT, Mg, NEFA, P, K, SDH, Na, tCO2, TP).
Chemistry_VDL_Reference_Range_Species: The species
that the VDL reports their reference ranges from. Our VDL reference
ranges were set to domesticated sheep reference ranges.
VDL_Chemistry_Sample_Type: Sample type that was
submitted for chemistry values.
VDL_Chemistry_Accession_Number_Specimen: The VDL’s
accession number followed by a sample number linking each individual’s
report to a unique number.
BUN: Blood Urea nitrogen (mg/dL). VDL reference
range 10 - 35mg/dL. In a study by Borjesson et al. 2000, reference
intervals for free-ranging bighorn sheep for 5 - 28 mg/dL (n = 200).
Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 6.4 - 28.6
mg/dL.
Creatinine: Creatinine (mg/dL). VDL reference range
0.9 - 2.0mg/dL. In a study by Borjesson et al. 2000, reference intervals
for free-ranging bighorn sheep for 1.6 - 2.6 mg/dL (n = 200). Reference
values for Borjesson et al. 2000 were calculated with nonparametric
analysis using the central 90th percentile. Southeast Oregon bighorn
sheep reference values (nonparametric) are 1.1 - 2.5 mg/dL.
Glucose: Glucose (mg/dL). VDL reference ranges 50 -
85 mg/dL. In a study by Borjesson et al. 2000, reference intervals for
free-ranging bighorn sheep for 95 - 185 mg/dL (n = 200). Reference
values for Borjesson et al. 2000 were calculated with nonparametric
analysis using the central 90th percentile. Southeast Oregon bighorn
sheep reference values (nonparametric) are 78.8 - 222.4 mg/dL.
Cholesterol: Cholesterol (mg/dL). VDL reference
ranges 40 - 76 mg/dL. Reference values for Borjesson et al. 2000 were
calculated with nonparametric analysis using the central 90th
percentile. Southeast Oregon bighorn sheep reference values
(nonparametric) are 28.6 - 76.0 mg/dL.
Triglycerides: Triglycerides (mg/dL). No standard
reported reference range by VDL. Southeast Oregon bighorn sheep
reference values (nonparametric) are 71.2 - 536.4 mg/dL.
Total_Protein: Total Protein (g/dL). VDL reference
ranges are 5.5 - 7.5 g/dL. In a study by Borjesson et al. 2000,
reference intervals for free-ranging bighorn sheep for total protein was
6.0 - 9.4 (n = 184) for adult sheep. Reference values for Borjesson et
al. 2000 were calculated with nonparametric analysis using the central
90th percentile. Southeast Oregon bighorn sheep reference values
(nonparametric) are 4.94 - 8.72 g/dL.
Albumin: Albumin (g/dL). VDL reference ranges are
2.5 - 3.9 g/dL. In a study by Borjesson et al. 2000, reference intervals
for free-ranging bighorn sheep for albumin was 2.8 - 3.7 g/dL (n = 200).
Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 2.54 - 4.42
g/dL.
Globulins: GLobulins (g/dL). Globulins were not
calculated by the VDL, nor were reference ranges reported. In a study by
Borjesson et al. 2000, reference intervals for free-ranging bighorn
sheep for globulins were 2.8 - 6.1 g/dL (n = 184) for adults and was 0.8
- 1.3 g/dL for young animals (n = 16). Reference values for Borjesson et
al. 2000 were calculated with nonparametric analysis using the central
90th percentile.
Albumin_Globulin_Ratio: The albumin to globulin
ratio. In a study by Borjesson et al. 2000, reference intervals for
free-ranging bighorn sheep for albumin:globulin ratios was 0.5 - 1.2 (n
= 184) for adults and was 0.8 - 1.3 for young animals (n = 16).
Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile.
Bilirubin: Total bilirubin (mg/dL). VDL reference
ranges are .0 - 0.5 mg/dL. In a study by Borjesson et al. 2000,
reference intervals for free-ranging bighorn sheep for total bilirubin
was 0.0 - 0.1 mg/dL (n = 200). Reference values for Borjesson et
al. 2000 were calculated with nonparametric analysis using the central
90th percentile. Southeast Oregon bighorn sheep reference values
(nonparametric) are 0.10 - 0.40 mg/dL.
CK: Creatine Kinase (U/L). VDL reference ranges are
50 - 150 U/L. In a study by Borjesson et al. 2000, reference intervals
for free-ranging bighorn sheep for CK were 175 - 2300 U/L (n = 200).
Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 16.8 - 1868.4
U/L.
GGT: Gamma-glutamyl Transferase (U/L). VDL reference
ranges are 30 - 94 U/L. In a study by Borjesson et al. 2000, reference
intervals for free-ranging bighorn sheep for GGT are 20 - 130 U/L (n =
200). Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 14.0 - 78.6
U/L.
AST: Aspartate transaminase (U/L). VDL reference
ranges are 60 - 110 U/L. In a study by Borjesson et al. 2000, reference
intervals for free-ranging bighorn sheep for ALT were 78 - 312 U/L (n =
200). Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 84 - 310.6
U/L.
Sodium: Sodium (mEq/L). VDL reference ranges are 145
- 155 mEq/L. In a study by Borjesson et al. 2000, reference intervals
for free-ranging bighorn sheep for sheep were 145 - 160 mmol/L (n =
200). Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 117.6 - 178.8
mEq/L.
Potassium: Potassium (mEq/L). VDL reference ranges
are 4.5 - 6.0 mEq/L. In a study by Borjesson et al. 2000, reference
intervals for free-ranging bighorn sheep for potassium were 3.8 - 6.3
mmol/L (n = 200). Reference values for Borjesson et al. 2000 were
calculated with nonparametric analysis using the central 90th
percentile. Southeast Oregon bighorn sheep reference values
(nonparametric) are 3.60 - 7.28 mEq/L.
Chloride: Chloride (mEq/L). VDL reference ranges are
95 - 112 mEq/L. In a study by Borjesson et al. 2000, reference intervals
for free-ranging bighorn sheep for Chloride were 89 - 107 mmol/L (n =
200). Reference values for Borjesson et al. 2000 were calculated with
nonparametric analysis using the central 90th percentile. Southeast
Oregon bighorn sheep reference values (nonparametric) are 78.2 - 115.6
mEq/L.
Calcium: Calcium (mg/dL). VDL reference ranges are
8.5 - 12.0 mg/dL. In a study by Borjesson et al. 2000, reference
intervals for free-ranging bighorn sheep for calcium were 9.3 - 11.5
mg/dL (n = 200). Reference values for Borjesson et al. 2000 were
calculated with nonparametric analysis using the central 90th
percentile. Southeast Oregon bighorn sheep reference values
(nonparametric) are 7.34 - 12.60 mg/dL.
Phosphorus: Phosphours (mg/dL). VDL reference ranges
are 5.0 - 7.5 mg/dL. In a study by Borjesson et al. 2000, reference
intervals for free-ranging bighorn sheep for phosphorus were 4.0 - 9.3
mg/dL (n = 200). Reference values for Borjesson et al. 2000 were
calculated with nonparametric analysis using the central 90th
percentile. Southeast Oregon bighorn sheep reference values
(nonparametric) are 2.96 - 8.62 mg/dL.
Magnesium: Magnesium (mg/dL). VDL reference ranges
are 2.2 - 2.8 mg/dL. No reference ranges were reported for Mg in
Borjesson et al. 2000. Southeast Oregon bighorn sheep reference values
(nonparametric) are 2 - 3.66 mg/dL.
tCO2: Total Carbon Dioxide (mEq/L). VDL reference
ranges are 21.0 - 28.0. No reference ranges were reported for tCO2 in
Borjesson et al. 2000. Southeast Oregon bighorn sheep reference values
(nonparametric) are 0.44 - 15.0 mEq/L.
BHbA: Beta-hydroxybutyrate (mg/dL). No reported
reference ranges at VDL. No reference ranges were reported for BHbA in
Borjesson et al. 2000. Southeast Oregon bighorn sheep reference values
(nonparametric) are 1.29 - 3.63 mg/dL.
Non_Esterfied_Fatty_Acids: Non_Esterfied_Fatty_Acids
(mEq/L). No reported VDL reference ranges. No reported ranges for
California Bighorn sheep. No reference ranges were reported for non
esterfied fatty acids in Borjesson et al. 2000.
Anion_Gap: Anion Gap reported in mEq/L. No reported
reference range by VDL. Normal anion gap reported for bovines is 19 -
26. Based off of the normal reference ranges for electrolytes in
Borjessen et al. 2000, the normal normal anion gap would be the
following:
SDH: Sorbitol_dehydrogenas (U/L). VDL reference
ranges are 6.0 - 27.0 U/L. Southeast Oregon bighorn sheep reference
values (nonparametric) are 11.16 - 114.79 U/L.
Chemistry_Laboratory: Laboratory that ran blood
chemistry values. VDL is the Carlson College of Veterinary Medicine
Veterinary Diagnostic Lab.
CBC_Personnel: Initials of person performing CBC
differential count.
Neutrophils: The percent neutrophils on WBC
differential count.
Lymphocytes: The percent lymphocytes on WBC
differential count.
Monocytes: The percent Monocytes on WBC differential
count.
Eosinophils: The percent Eosinophils on WBC
differential count.
Basophils: The percent Basophils on WBC differential
count.
Bands: The percent bamded neutrophils on WBC
differential count.
Metamyelocytes: The percent Metamyelocytes on WBC
differential count.
Neutrophil_Toxicity: A subjective rating of degree
of neutrophil toxicity as determined by clinical pathologist. Possible
values are 0 (no toxic changes noted), 1, 2, and 3 (highest degree of
toxic changes noted).
Lymphocyte Reactivity: A subjective rating of degree
of lymphocyte reactivity as determined by clinical pathologist. Possible
values are 0 (no reactive changes noted), 1, 2, and 3 (highest degree of
reactive changes noted).
Anaplasma: A rating of degree of anaplasma infection
present in blood smear where 0 means no anaplasma infection was noted
and 3 being the highest numbers of Anaplasma were noted in peripheral
blood sample.
CBC_Differential_Total: Sum of percentages obtained
for differential WBC count. Should sum to 100%
Fecal_Egg_Count_Sample_Weight_g: Grams of fecal
sample used for fecal egg counts.
Fecal_Egg_Count_Ascaris: Fecal egg count
ascaris.
Fecal_Egg_Count_Strongyle: Fecal egg count
strongyle.
Fecal_Egg_Count_Coccidia: Fecal egg count
coccidia.
Fecal_Egg_Count_Trichuris: Fecal egg count
trichuris.
Fecal_Egg_Count_Pinworm: Fecal egg count
pinworm.
Fecal_Egg_Count_Cestode: Fecal egg count
cestode.
Fecal_Egg_Count_Process_Date: Date fecal egg counts
were performed.
Fecal_Egg_Count_Notes: Notes from field technition
about Fecal egg counts.
Serology_AM_ELISA:
Se: Selenium ppm in whole blood EDTA from UC Davis
CAHFS Report D2014031. Reporting limit is the lowest routinely
quantified concentration of an analyte in a sample. The analyte may be
detected, but not quantified at concentrations that are below the
reporting limit. Sample volumes less than requested might result in
reporting limits that are higher than those listed. Reporting limit
0.010 ppm. Reference range reported is 0.08 to 0.5.
Se_Specimen: The sample that was used for by the
laboratory for selenium.
Se_Lab: Lab that reported Se column.
Se_Lab_Accession: Lab accession number from
Se_Lab.
Se_Units: Units that Se is reported
in.
BRSV_Status: Bovine Respiratory Syncytial Virus
Antibody Immunofluorescence Assay (IFA) Results. Based on the clinical
interpretation suggested is that 1:40 is evidence for exposure /
infection in domesticated livestock. They classify into
semi-quantitative categories:
BRSV_Titer result.BRSV_Titer: Titer reported along with
BRSV_Status.
BRSV_Specimen: Sample used for
BRSV_Status.
BRSV_Lab: Laboratory that ran
BRSV_Status results are from UC Davis CAHFS Report
D2014031.
BRSV_Lab_Accession: Lab accession number from
BRSV_Status.
BRSV_Test: Test type for results presented in
BRSV_Stats and BRSV_Titer column.
CE_Status: Contagious Ecthyma Antibody Results
reported via compliment fixation (CF). Based on clinical interpretation,
the CDFW may report these as:
Note that for the current dataset, I encoded CE_Status as reported by
UC Davis CAHFS Report D2014031 and not by CDFW semi-quantitative values
discussed above for clinical interpretation. See paired column
CE_CF.
CE_CF: Complement fixation number paired with
CE_Status above.
CE_Specimen: Sample type used for
CE_Status.
CE_Lab: Lab that ran the test for
CE_Status above.
CE_Test: Test type used for
CE_Status.
BT_EHD_Status: Test result from Bluetongue Virus /
Epizootic Hemorrhage Disease antibody agar gel immunodiffusion (AGID)
assay as reported by UC Davis CAHFS Report D2014031. Results are
reported as positive or negative only.
BT_EHD_Specimen: Specimen type for
BT_EHD_Status.
BT_EHD_Lab: Lab reporting
BT_EHD_Status.
BT_EHD_Lab_Accession: Accession number of report for
BT_EHD_Status.
BT_EHD_Test: Test type of
BT_EHD_Status.
BT_Status: Test result from Bluetongue virus
antibody enzyme linked immunosorbent assay (cELISA) as reported by UC
Davis CAHFS report D2014031. Results are reported as positive or
negative only.
BT_Specimen: Specimen type for
BT_Status.
BT_Lab: Lab reporting
BT_Status.
BT_Lab_Accession: Accession number of report for
BT_Status.
BT_Test: Test type of
BT_Status.
PI3_Status: Parainfluenza 3 (PI-3) antibody
hemaglutination inhibition (HI) as reported by UC Davis CAHFS report
D2014031. Clincial interpreation suggested doesn’t differ based on the
results shown here.
PI3_Titer: Titer result for
PI3_Status.
PI3_Specimen: Specimen type for
PI3_Status.
PI3_Lab: Laboratory that reports
PI3_Status.
PI3_Lab_Accession: Lab accession number for
PI3_Status.
PI3_Test: Test type for
PI3_Status.
Am_Status:
Am_Specimen:
Am_Lab:
Am_Lab_Accession:
Am_Test:
``:
\[233\] “”
\[234\] “”
\[235\] “”
\[236\] “”
\[237\] “”
\[238\] “”
\[239\] “IBR_Status”
\[240\] “IBR_Titer”
\[241\] “IBR_Specimen”
\[242\] “IBR_Lab”
\[243\] “IBR_Lab_Accession”
\[244\] “IBR_Test”
\[245\] “BVDV1_Status”
\[246\] “BVDV1_Titer”
\[247\] “BVDV1_Specimen”
\[248\] “BVDV1_Lab”
\[249\] “BVDV1_Lab_Accession”
\[250\] “BVDV1_Test”
\[251\] “BVDV2_Status”
\[252\] “BVDV2_Titer”
\[253\] “BVDV2_Specimen”
\[254\] “BVDV2_Lab”
\[255\] “BVDV2_Lab_Accession”
\[256\] “BVDV2_Test”
\[257\] “Ch_Status”
\[258\] “Ch_Titer”
\[259\] “Ch_Specimen”
\[260\] “Ch_Lab”
\[261\] “Ch_Lab_Accession”
\[262\] “Ch_Test”
infectious_Bovine_rhinotracheatiis_titer bovine_viral_diarrhea_titer Serum neutralization parainfluenza titer parainflenza ISOlation Parainflenza hi bluetoung elisa agid bt ioslation epizoatic hemorrhagic disease isolation brucellossis lepto each of lepto titers
bovine resp synctial virus ovine progressive pneumonia anaplasma card anaplasma elisa toxoplasmosis titer chlymidia orf Mycoplasma ovipneumonia WSUT diagnostic and WSUE diagnostic
Mycoplasma ovipneumoniae https://tests.waddl.vetmed.wsu.edu/Tests/Details/8147
California Bighorn Sheep Reference Intervals:
Confidence intervals for chemistry data parameters for California
bighorn sheep. The particular population of California bighorn sheep is
geographically located in our Oregon study system.
Bighorn Sheep Chemistry Reference Ranges: A file of
calculated chemistry reference intervals calculated from various bighorn
sheep populations.
Desert Bighorn Sheep Fecal Egg Counts 2020: A file
of fecal egg counts performed in the field for desert bighorn
sheep.
Toxicology_Serology_Disease_Panel_CAHFS_UCDavis_D2014031_HKA:
Serology results from UCDavis report number D2014031. Results have been
crosschecked by HKA and MFW.
Toxicology_Serology_Disease_Panel_Clinical_Interpretation:
Clinical interpretation of what titer values mean from serology results.
Note that the status reported by UCDavis (e.g. “positive”) might not
match the values that they suggest here for use as positive or negative
animals. Annotated this readme file from the UCDavis disease panel
results with this info.
Serology Mojave 1980-2020: Latest serology data
taken from Sara Carpenter email sent on 3/10/2023 with attachment
“Serology Mojave 1980-2017_SC 2.csv”. I did not integrate this into my
analysis because it is encoded in a manner specific for integration with
the other disease panel results that are encoded by the CDFW.
Codes for positive and negative results include:
0 Not done or sample was contaminated 1 Negative 2 Suspect 3 Positive
Codes for titer results include:
0 Not done 1 Negative
Titers are the number of the titer’s reciprocal (i.e. 64 for 1:64)
Age
0 Not known 1 0 to 2 years 2 >2 years
Sex
0 not known 1 male 2 female