Salmonella report

Overiview of the data

Quality trimming summary Reads are trimmed from the right with a minimum Phred score of 20 to a minimum length of 180. Then left & right homopolymers are trimmed.

stage	reads	bases
original	280,370	70,092,500
filtered	232,742	57,123,859

Mapping

1. Map 232,742 reads at 100% identity allowing for multiple positions:

   Canu
   pb_636_20
   statistic	100% identity + secondary
   reads mapped	155,574
   bases mapped	38,328,553
   ref covered	4,620,743
   ref uncovered	31,377
   gaps	464

   
   155,574 map perfectly in at least 1 place, 77,168 reads have not yet been mapped.
   
   To visualize where the gaps are in the alignment, we can look at the sum of all gaps within each 100 Kb portion of the reference genome:
   
   Subsequent mapping steps will fill in these gaps and show which have variants.
   
2. Map the 155,574 reads at 100% and identify reads with multiple sites

Canu
pb_636_20
type	reads	bases
unmapped:	1,342	331,590
mapped:	155,568	38,327,062

The 1,342 reads were remapped at 80% identity and no variants were found.

3. The 77,168 reads can now be mapped at 95% identity (no multiple alignments)
Identify how many reads mapped and how much more genome is covered:

Canu
pb_636_20
statistic	100% identity + secondary + 95% identity
reads mapped	26,469
bases mapped	6,456,783
ref covered	4,631,605
ref uncovered	20,515
gaps	337

Call variants in the gap regions:

Canu
pb_636_20_95pid
Molecule	Pos	Ref	Alt	Qual	Type	ref_seq	alt_seq
canu	180,936	C	CG	34.63	INS	TATGACTTTGCCGGGGTTTTCGC	TATGACTTTGCCGGGGGTTTTCGC
canu	734,742	A	G	22.89	SUB	TTCTTCATTGCACTCAGTCTGTT	TTCTTCATTGCGCTCAGTCTGTT
canu	1,110,949	T	TA	38.50	INS	ACAGCATCTAATAAAAAGAGAAA	ACAGCATCTAATAAAAAAGAGAAA
canu	1,437,932	C	A	22.55	SUB	CGGTGCAGCAACTCATGCAGACG	CGGTGCAGCAAATCATGCAGACG
canu	1,731,702	C	G	27.93	SUB	CTTCTGAATATCGTGGCGGGCGT	CTTCTGAATATGGTGGCGGGCGT
canu	1,917,704	G	GC	38.52	INS	ACATCATCTCTGCCCCCGGGCAA	ACATCATCTCTGCCCCCCGGGCAA
canu	2,058,140	A	T	22.20	SUB	GGCGCGACCATATTCCCCAGCCC	GGCGCGACCATTTTCCCCAGCCC
canu	2,595,883	C	A	22.17	SUB	CGCCTTGCGCGCCGGGCACGTTG	CGCCTTGCGCGACGGGCACGTTG
canu	2,672,224	C	T	22.84	SUB	GGTAAACCCGTCACGGAAACGCT	GGTAAACCCGTTACGGAAACGCT
canu	2,738,375	A	AC	27.91	INS	GTGATGTCATAACCCCCCCCTTT	GTGATGTCATAACCCCCCCCCTTT
canu	2,794,618	T	TC	37.75	INS	TAAAACGCTTTTCCCCATCCAAT	TAAAACGCTTTTCCCCCATCCAAT
canu	3,144,273	C	T	27.33	SUB	TGCTGGACCGCCTTCTGGTAGAC	TGCTGGACCGCTTTCTGGTAGAC
canu	4,529,193	T	C	22.64	SUB	CTCACGCTGGCTGTCCTGCGCAG	CTCACGCTGGCCGTCCTGCGCAG

4. The remaining 50,699 reads are mapped at 80% (allowing multiple alignments):

Canu
pb_636_20
statistic	(100% + secondary) + 95% + (80% + secondary)
reads mapped	44,316
bases mapped	10,855,244
ref covered	4,640,362
ref uncovered	11,758
gaps	230

There were 235 new variants detected using the 80% reads.
So in total, the reconstruction will have 248 variants found and 11,758 nt of unverified bases.
The remaining 6,383 unmapped reads will be de novo assembled and blasted.