Built data using BWA to estimate CRM2 (Centromereic Retrotransposon of Maize) abundance in sequenced maize lines from Jiao et al (2012)
Get raw data from tab delimited table.
setwd("/Users/Sid/Projects/")
x = read.table("Jiao_CRM2_abun_complete.stat", header = T)
print(x)
## Line Accession Total_Reads Reads_Mapped
## 1 CAU06_zong31 SRR448305.sra 70219816 70220
## 2 CAU07_D340 SRR448306.sra 66386418 54178
## 3 CAU08_H127 SRR448307.sra 62268792 49130
## 4 CAU10_yu87-1 SRR448310.sra 73665576 81314
## 5 CAU100_shen5005 SRR448311.sra 12737252 11872
## 6 CAU103_807D SRR448312.sra 16300934 16898
## 7 CAU105_1145 SRR448313.sra 24718516 24168
## 8 CAU105_1145 SRR448314.sra 30564896 30084
## 9 CAU107_D15 SRR448315.sra 53675218 47086
## 10 CAU11_longkang11 SRR448316.sra 71101708 65244
## 11 CAU112_S22 SRR448317.sra 27845610 23814
## 12 CAU114_Q1261 SRR448318.sra 43455832 41566
## 13 CAU115_ye52106 SRR448319.sra 50490050 39144
## 14 CAU116_1205A SRR448320.sra 54763896 47004
## 15 CAU118_K12 SRR448321.sra 66030204 53400
## 16 CAU12_danhuang02 SRR448322.sra 70335690 64104
## 17 CAU120_xing230 SRR448324.sra 37385070 34578
## 18 CAU125_K22 SRR448325.sra 27629178 26368
## 19 CAU125_K22 SRR448326.sra 30776512 29822
## 20 CAU129_P007 SRR448328.sra 24565994 19752
## 21 CAU131_Yd6 SRR448332.sra 39416476 37072
## 22 CAU132_IA5125 SRR448333.sra 34932284 21530
## 23 CAU133_liao2202 SRR448334.sra 11502010 9012
## 24 CAU134_dai6 SRR448336.sra 31280364 28016
## 25 CAU137_W499 SRR448337.sra 34393388 32040
## 26 CAU14_shen137 SRR448338.sra 47486836 44720
## 27 CAU140_XOP2 SRR448340.sra 44223166 39012
## 28 CAU142_D20 SRR448341.sra 38019170 39502
## 29 CAU143_hai1134 SRR448342.sra 42870590 40144
## 30 CAU144_yu374 SRR448343.sra 32233382 29748
## 31 CAU146_dan9064 SRR448344.sra 49368884 46352
## 32 CAU147_niu2-1 SRR448345.sra 13537904 13490
## 33 CAU148_suwan1611 SRR448346.sra 43960032 45606
## 34 CAU149_R017 SRR448347.sra 34029830 31680
## 35 CAU15_zheng22 SRR448348.sra 29773608 23152
## 36 CAU151_shen977 SRR448349.sra 19930138 17404
## 37 CAU156_huangchangb SRR448350.sra 11487270 10176
## 38 CAU16_lv28 SRR448351.sra 57672880 56364
## 39 CAU164_K10 SRR448352.sra 19345838 15948
## 40 CAU165_ye5237 SRR448353.sra 24707316 20798
## 41 CAU166_zheng32 SRR448354.sra 52534964 59814
## 42 CAU17_huangC SRR448355.sra 57496794 56592
## 43 CAU173_P167 SRR448356.sra 28673978 27282
## 44 CAU174_R31 SRR448357.sra 23611472 21184
## 45 CAU178_changK SRR448358.sra 94898024 71550
## 46 CAU18_P138 SRR448359.sra 20583530 16476
## 47 CAU180_M131-5 SRR448360.sra 61677804 55892
## 48 CAU19_zi330 SRR448361.sra 20203698 15332
## 49 CAU191_hai014 SRR448362.sra 29484904 29602
## 50 CAU192_ji444 SRR448363.sra 32386756 27488
## 51 CAU193_ben7884 SRR448364.sra 26833726 21706
## 52 CAU194_huangyesi3 SRR448365.sra 54763730 45388
## 53 CAU195_zaC546 SRR448366.sra 26946532 21776
## 54 CAU197_4F1 SRR448367.sra 54015334 53664
## 55 CAU198_wenhuang31413 SRR448368.sra 40507588 37282
## 56 CAU199_ye515 SRR448369.sra 28398802 27742
## 57 CAU20_huangzaosi SRR448370.sra 191107860 142662
## 58 CAU200_hu803 SRR448371.sra 30856650 30090
## 59 CAU201_tian77 SRR448372.sra 25134256 24228
## 60 CAU202_ye488 SRR448373.sra 34012968 30114
## 61 CAU203_chang72 SRR448388.sra 34950426 33198
## 62 CAU207_3H2 SRR448389.sra 30423952 25500
## 63 CAU208_cheng698-3 SRR448390.sra 45204634 35120
## 64 CAU21_tie7922 SRR448391.sra 34600798 32792
## 65 CAU210_su75 SRR448392.sra 22677324 20362
## 66 CAU211_Beck SRR448393.sra 24570698 19410
## 67 CAU215_P136 SRR448394.sra 21826386 13586
## 68 CAU217_dan9046 SRR448395.sra 110652394 79300
## 69 CAU224_W64a SRR448397.sra 28249538 25178
## 70 CAU225_A554 SRR448398.sra 22544530 20572
## 71 CAU229_xun92-8 SRR448399.sra 25270368 26564
## 72 CAU234_H21 SRR448400.sra 887248 692
## 73 CAU234_H21 SRR448401.sra 16068844 11060
## 74 CAU235_shuang741 SRR448444.sra 559588 448
## 75 CAU235_shuang741 SRR448445.sra 15585524 12014
## 76 CAU236_200B SRR448446.sra 1092870 988
## 77 CAU236_200B SRR448447.sra 30213536 22898
## 78 CAU237_chong72 SRR448490.sra 770168 526
## 79 CAU237_chong72 SRR448491.sra 15903990 12240
## 80 CAU238_Pa91 SRR448492.sra 1329132 1110
## 81 CAU238_Pa91 SRR448493.sra 17088306 16402
## 82 CAU239_yu537A SRR448494.sra 1133342 978
## 83 CAU239_yu537A SRR448495.sra 17187062 17022
## 84 CAU24_9058 SRR448496.sra 31221240 22574
## 85 CAU242_dan3115 SRR448497.sra 38457172 38896
## 86 CAU244_zhonghuang64 SRR448522.sra 37820058 31698
## 87 CAU247_dong327 SRR448565.sra 19962552 17746
## 88 CAU248_698-3 SRR448566.sra 40650728 33600
## 89 CAU248_698-3 SRR448567.sra 23408544 19788
## 90 CAU25_ji853 SRR448568.sra 32828864 31344
## 91 CAU251_N138 SRR448569.sra 28308546 23164
## 92 CAU251_N138 SRR448570.sra 27426684 22700
## 93 CAU254_DM07 SRR448571.sra 15858484 13626
## 94 CAU254_DM07 SRR448572.sra 28582924 25054
## 95 CAU256_B100 SRR448573.sra 14947500 9582
## 96 CAU257_B98 SRR448576.sra 60212028 54146
## 97 CAU261_lian87 SRR448577.sra 18753222 16086
## 98 CAU264_L-1 SRR448579.sra 23719324 22018
## 99 CAU271_changD SRR448584.sra 40051050 32926
## 100 CAU273_M101 SRR448592.sra 29879810 27370
## 101 CAU275_B394 SRR448595.sra 24172980 18620
## 102 CAU282_R25 SRR448597.sra 20020758 16774
## 103 CAU282_R25 SRR448599.sra 20382750 16744
## 104 CAU283_chengzi108 SRR448600.sra 45166164 38330
## 105 CAU289_ye107 SRR448601.sra 12277680 9334
## 106 CAU289_ye107 SRR448603.sra 37127890 28178
## 107 CAU29_Maxa SRR448604.sra 23784756 18664
## 108 CAU290_jiutai1 SRR448605.sra 35612130 30134
## 109 CAU294_hai9-21 SRR448624.sra 24425646 20866
## 110 CAU295_ji533 SRR448625.sra 16621920 13066
## 111 CAU297_ye832 SRR448626.sra 11569580 11824
## 112 CAU302_B76 SRR448627.sra 7816276 6338
## 113 CAU302_B76 SRR448628.sra 15188982 14420
## 114 CAU303_NC268 SRR448629.sra 10264424 8234
## 115 CAU303_NC268 SRR448630.sra 19439364 15016
## 116 CAU306_Sg1533 SRR448631.sra 6545594 4888
## 117 CAU306_Sg1533 SRR448632.sra 13833628 9470
## 118 CAU310_7327 SRR448635.sra 26323878 20258
## 119 CAU316_bao3040 SRR448636.sra 28374614 30016
## 120 CAU320_Lx9801 SRR448637.sra 1351970 1076
## 121 CAU320_Lx9801 SRR448638.sra 14739538 15662
## 122 CAU326_shen135 SRR448639.sra 72490194 67162
## 123 CAU332_baihe43 SRR448640.sra 18218254 16070
## 124 CAU34_nan21-3 SRR448641.sra 33345152 40472
## 125 CAU345_jiu138-5 SRR448642.sra 49171122 46238
## 126 CAU347_ning55 SRR448643.sra 29692712 27624
## 127 CAU350_han21 SRR448644.sra 28291238 23204
## 128 CAU355_huotanghuang SRR448645.sra 33904366 29942
## 129 CAU357_yu82 SRR448646.sra 24306144 20270
## 130 CAU359_CN165 SRR448647.sra 20754496 17664
## 131 CAU361_fu8701 SRR448648.sra 20774778 17968
## 132 CAU362_De811 SRR448649.sra 15495998 11314
## 133 CAU365_shan89 SRR448651.sra 22904378 22028
## 134 CAU366_A679 SRR448652.sra 20135748 18924
## 135 CAU367_Va26 SRR448653.sra 18801134 15986
## 136 CAU370_E28 SRR448654.sra 15454280 12590
## 137 CAU372_zhongyin15 SRR448655.sra 10654558 8608
## 138 CAU372_zhongyin15 SRR448656.sra 16365804 13498
## 139 CAU375_zong3 SRR448657.sra 22163646 16210
## 140 CAU382_FC-13 SRR448658.sra 22840942 23276
## 141 CAU384_ji63 SRR448659.sra 1262776 944
## 142 CAU384_ji63 SRR448660.sra 19467988 13230
## 143 CAU385_ji434 SRR448661.sra 34082138 27964
## 144 CAU386_ji4112 SRR448662.sra 1284584 938
## 145 CAU386_ji4112 SRR448663.sra 25486136 20664
## 146 CAU389_qi205 SRR448664.sra 14425640 12072
## 147 CAU40_B68 SRR448665.sra 13638468 11430
## 148 CAU400_P25 SRR448666.sra 32415118 29636
## 149 CAU401_R98 SRR448667.sra 26702646 24114
## 150 CAU402_qi319 SRR448668.sra 9176752 8550
## 151 CAU402_qi319 SRR448669.sra 17924678 15682
## 152 CAU405_huo17 SRR448670.sra 28841646 26116
## 153 CAU409_huangyesi SRR448671.sra 37093762 30200
## 154 CAU411_shen142 SRR448672.sra 21734676 20264
## 155 CAU413_siyi SRR448673.sra 19036904 13878
## 156 CAU416_xun971 SRR448674.sra 15462348 15264
## 157 CAU420_Mo24W SRR448676.sra 33120802 34348
## 158 CAU422_W182bn SRR448678.sra 26009118 21176
## 159 CAU423_W153R SRR448679.sra 9777048 9782
## 160 CAU423_W153R SRR448680.sra 16824690 16008
## 161 CAU425_HP301 SRR448682.sra 11084624 7902
## 162 CAU425_HP301 SRR448684.sra 13859378 9562
## 163 CAU426_H84 SRR448685.sra 17188970 15370
## 164 CAU429_tangsipingtou SRR448693.sra 38787646 29130
## 165 CAU434_cheng18 SRR448742.sra 49272734 41764
## 166 CAU436_xinlun5-9 SRR448743.sra 13084908 10194
## 167 CAU439_lv45 SRR448744.sra 19311120 18822
## 168 CAU446_fengke1 SRR448745.sra 16977582 18986
## 169 CAU448_ernan24 SRR448788.sra 51042346 46924
## 170 CAU451_78371A SRR448789.sra 38269034 28448
## 171 CAU452_PHT10 SRR448790.sra 27149010 26268
## 172 CAU453_PHH93 SRR448831.sra 16415530 11682
## 173 CAU454_IBB14 SRR448832.sra 17226950 14212
## 174 CAU458_LH149 SRR448879.sra 3309522 2946
## 175 CAU458_LH149 SRR448880.sra 25018072 23976
## 176 CAU461_794 SRR448881.sra 7734988 6252
## 177 CAU461_794 SRR448922.sra 30834598 22940
## 178 CAU463_PHR32 SRR448923.sra 24227956 17086
## 179 CAU465_PHG50 SRR448924.sra 2383588 1646
## 180 CAU465_PHG50 SRR448925.sra 27007036 22730
## 181 CAU466_LH51 SRR448926.sra 24417620 18662
## 182 CAU468_78010 SRR448927.sra 24898596 28054
## 183 CAU470_LH39 SRR448928.sra 47102974 35486
## 184 CAU471_PHG84 SRR448929.sra 19108702 15300
## 185 CAU475_LH57 SRR448930.sra 1320746 846
## 186 CAU475_LH57 SRR448931.sra 32340334 26098
## 187 CAU476_LH38 SRR448935.sra 7391476 6122
## 188 CAU476_LH38 SRR448937.sra 25278216 20096
## 189 CAU488_807 SRR448938.sra 3143058 2562
## 190 CAU488_807 SRR448939.sra 44471184 40680
## 191 CAU489_OH43 SRR448940.sra 34758850 27942
## 192 CAU490_PHN11 SRR448941.sra 27764940 23562
## 193 CAU491_PHJ70 SRR448942.sra 15360396 14508
## 194 CAU492_DJ7 SRR448943.sra 14545486 13486
## 195 CAU496_790 SRR448944.sra 15964582 14336
## 196 CAU497_PHZ51 SRR448945.sra 11057414 9290
## 197 CAU497_PHZ51 SRR448946.sra 37099230 36304
## 198 CAU498_PHT60 SRR448947.sra 14620536 10880
## 199 CAU501_PHG83 SRR448948.sra 24887488 23948
## 200 CAU503_PHJ75 SRR448950.sra 24187540 17402
## 201 CAU505_PB80 SRR448951.sra 21949448 21494
## 202 CAU510_LH52 SRR448952.sra 2438418 1812
## 203 CAU510_LH52 SRR448953.sra 25145524 23258
## 204 CAU513_PHW52 SRR448954.sra 10101170 7306
## 205 CAU513_PHW52 SRR448955.sra 19176164 13762
## 206 CAU514_LH93 SRR448956.sra 17886148 14650
## 207 CAU515_PHM57 SRR448957.sra 18103124 18998
## 208 CAU517_LH60 SRR448958.sra 11517712 8202
## 209 CAU518_PHG71 SRR448959.sra 6427348 5192
## 210 CAU518_PHG71 SRR448960.sra 20754030 12678
## 211 CAU520_Q381 SRR448961.sra 5625562 4450
## 212 CAU520_Q381 SRR448962.sra 34875494 26368
## 213 CAU521_MBPM SRR448963.sra 3765414 3050
## 214 CAU521_MBPM SRR449014.sra 38729504 19122
## 215 CAU522_PHW03 SRR449015.sra 4237776 3156
## 216 CAU522_PHW03 SRR449016.sra 42496296 21406
## 217 CAU523_PHW43 SRR449084.sra 4698024 4418
## 218 CAU523_PHW43 SRR449085.sra 24875338 21050
## 219 CAU525_LH190 SRR449086.sra 19367306 16752
## 220 CAU526_B47 SRR449087.sra 16624604 14944
## 221 CAU527_PHV78 SRR449088.sra 33792100 33244
## 222 CAU528 SRR449089.sra 26704916 23778
## 223 CAU530_PHK76 SRR449090.sra 15586120 14040
## 224 CAU531_LH1 SRR449091.sra 28823406 24380
## 225 CAU534_PHJ31 SRR449093.sra 6808270 6908
## 226 CAU534_PHJ31 SRR449094.sra 26942606 33050
## 227 CAU535_78002A SRR449095.sra 12329206 13272
## 228 CAU536_792 SRR449096.sra 15532588 14700
## 229 CAU537_PHJ40 SRR449097.sra 14269036 11920
## 230 CAU538_LH54 SRR449098.sra 29737068 24896
## 231 CAU539_FAPW SRR449099.sra 13815894 10808
## 232 CAU541_LH205 SRR449100.sra 6665354 6082
## 233 CAU541_LH205 SRR449101.sra 26842458 24404
## 234 CAU542_LH127 SRR449102.sra 6477142 6020
## 235 CAU542_LH127 SRR449103.sra 31737162 33484
## 236 CAU545_LH194 SRR449104.sra 8904602 7966
## 237 CAU545_LH194 SRR449105.sra 23459172 21320
## 238 CAU546_LH202 SRR449106.sra 12749888 11196
## 239 CAU549_RS710 SRR449107.sra 5357402 4062
## 240 CAU549_RS710 SRR449108.sra 37020394 24596
## 241 CAU551_PHW51 SRR449109.sra 4181706 2730
## 242 CAU551_PHW51 SRR449111.sra 33734362 30748
## 243 CAU566_PHP85 SRR449112.sra 2186570 1384
## 244 CAU566_PHP85 SRR449113.sra 40715694 42650
## 245 CAU572_LH143 SRR449114.sra 45251542 45960
## 246 CAU574_207 SRR449115.sra 32057702 27808
## 247 CAU575_CR1HT SRR449116.sra 22266226 20632
## 248 CAU576_6103 SRR449117.sra 31176454 28904
## 249 CAU578_4676A SRR449118.sra 22171696 17144
## 250 CAU580_PHR36 SRR449119.sra 15165134 13922
## 251 CAU582_IB02 SRR449120.sra 20362334 17788
## 252 CAU583_IBB15 SRR449121.sra 60631572 56720
## 253 CAU584_787 SRR449122.sra 23909270 18418
## 254 CAU586_11430 SRR449123.sra 31886404 27100
## 255 CAU587_2369 SRR449124.sra 21544254 17806
## 256 CAU588_2MA22 SRR449125.sra 17974302 16906
## 257 CAU590_MBST SRR449126.sra 41341714 33934
## 258 CAU591_PHN47 SRR449127.sra 27884408 25098
## 259 CAU592_NS501 SRR449128.sra 19970744 16752
## 260 CAU593_H8431 SRR449129.sra 19612446 17956
## 261 CAU594_S8324 SRR449130.sra 22411272 18896
## 262 CAU595_CR14 SRR449131.sra 20019684 16952
## 263 CAU596_WIL901 SRR449132.sra 18022358 14572
## 264 CAU597_WIL903 SRR449179.sra 20377400 16632
## 265 CAU598_WIL500 SRR449180.sra 15765472 14348
## 266 CAU599_E8501 SRR449181.sra 27138434 21156
## 267 CAU601_L135 SRR449183.sra 16290430 14000
## 268 CAU604_PHM10 SRR449184.sra 7783944 5356
## 269 CAU604_PHM10 SRR449185.sra 36024786 31238
## 270 CAU605_PHN82 SRR449186.sra 10175332 7640
## 271 CAU605_PHN82 SRR449187.sra 43682008 39964
## 272 CAU607_PHR63 SRR449188.sra 9367438 7276
## 273 CAU607_PHR63 SRR449189.sra 45047048 42452
## 274 CAU610_PHW20 SRR449190.sra 3260778 2256
## 275 CAU610_PHW20 SRR449191.sra 38412724 31804
## 276 CAU611_W23 SRR449192.sra 15964114 12086
## 277 CAU631_PHP55 SRR449193.sra 9445118 7252
## 278 CAU631_PHP55 SRR449194.sra 38110404 32388
## 279 CAU638_huobai SRR449195.sra 36451508 28776
## 280 CAU69_qi410 SRR449196.sra 1352992 1466
## 281 CAU77_DH149 SRR449198.sra 28236574 16102
## 282 CAU78_R08 SRR449199.sra 30134172 19306
## 283 CAU84_B95 SRR449200.sra 32188264 33296
## 284 CAU84_B95 SRR449201.sra 50933578 52886
## 285 CAU97_guan17-1 SRR449202.sra 13353680 9144
## 286 CAU98_wu125 SRR449203.sra 9470064 8658
## 287 CAU98_wu125 SRR449204.sra 24648332 21122
## 288 CAU31_wu126 SRR449205.sra 3671854 3084
## 289 CAU31_wu126 SRR449206.sra 30743310 28932
## 290 CAU33_yi36 SRR449207.sra 19094048 11480
## 291 CAU39_CM105 SRR449208.sra 35389274 29674
## 292 CAU41_P39 SRR449209.sra 21084332 11996
## 293 CAU42_shangyin110-1 SRR449210.sra 31503948 28720
## 294 CAU46_zhong451 SRR449211.sra 23256652 23364
## 295 CAU47_huotanghuang17 SRR449212.sra 8949604 10490
## 296 CAU47_huotanghuang17 SRR449213.sra 38993976 29166
## 297 CAU58_B12 SRR449214.sra 55059104 49908
## 298 CAU609_PHV37 SRR449215.sra 39491576 44116
## 299 CAU61_ji870 SRR449216.sra 12808268 12284
## 300 CAU63_fu8521 SRR449217.sra 2012666 2014
## 301 CAU63_fu8521 SRR449218.sra 21413840 15408
## 302 CAU68_jiao05 SRR449219.sra 39058972 40972
## 303 CAU73_xiangai3 SRR449244.sra 67539420 60112
## 304 CAU74_fusheA SRR449245.sra 49431430 55224
## 305 CAU76_qiong51 SRR449246.sra 56228928 58710
## 306 CAU547_LH191_1 SRR449248.sra 10951630 9104
## 307 CAU547_LH191_2 SRR449249.sra 23289192 17424
## 308 CAU548_LH192_1 SRR449264.sra 10372950 10668
## 309 CAU548_LH192_2 SRR449267.sra 14068490 14190
## 310 CAU577_IB014_1 SRR449268.sra 9392584 7534
## 311 CAU577_IB014_2 SRR449269.sra 11433200 8838
## 312 CAU581_NS701_1 SRR449271.sra 10179172 9902
## 313 CAU581_NS701_2 SRR449273.sra 9626492 9220
## 314 CAU589_87916W_1 SRR449274.sra 10859552 8980
## 315 CAU589_87916W_2 SRR449276.sra 8537844 6566
## 316 CAU606_PHP60_1 SRR449277.sra 10752754 8746
## 317 CAU606_PHP60_2 SRR449278.sra 7504736 4696
## 318 CAU38_A632 SRR449338.sra 54464596 46108
## 319 CAU38_A632 SRR449339.sra 199387832 167546
## 320 CAU01_zheng58 SRR449340.sra 209125210 201684
## 321 CAU01_zheng58 SRR449342.sra 209579908 201356
## 322 CAU01_zheng58 SRR449343.sra 208768408 201098
## 323 CAU02_chang7-2 SRR449344.sra 215501582 261894
## 324 CAU02_chang7-2 SRR449345.sra 218349742 264266
## 325 CAU02_chang7-2 SRR449346.sra 219074862 265270
## 326 CAU05_478 SRR449347.sra 202243146 202434
## 327 CAU05_478 SRR449348.sra 205326492 206170
## 328 CAU06_zong31 SRR449350.sra 71775184 71918
## 329 CAU07_D340 SRR449351.sra 65873364 53792
## 330 CAU08_H127 SRR449352.sra 62077718 49170
## 331 CAU04_5003 SRR449353.sra 208709388 189016
## 332 CAU04_5003 SRR449354.sra 206458284 186596
## 333 CAU04_5003 SRR449355.sra 203394280 182724
## 334 CAU27_ye8112_1 SRR449357.sra 72344528 80498
## 335 CAU27_ye8112_2 SRR449358.sra 72138478 80320
## 336 CAU27_ye8112_2 SRR449359.sra 72210448 80328
## 337 CAU196_ji846 SRR449427.sra 56594520 48646
## 338 Mo17 SRR449556.sra 58492968 47904
## 339 Mo17 SRR449557.sra 76515472 62026
## 340 Mo17 SRR449558.sra 84859158 69872
## 341 CAU27_ye8112_1 SRR528558.sra 70447254 78762
## 342 CAU05_478 SRR528559.sra 202710778 203214
## 343 CAU01_Zheng58_BGI_1 SRR530830.sra 36928096 34014
## 344 CAU01_Zheng58_BGI_1 SRR530831.sra 40903792 37698
## 345 CAU01_Zheng58_BGI_2 SRR530833.sra 60876800 60386
## 346 CAU05_478_BGI_1 SRR530834.sra 9272124 8282
## 347 CAU05_478_BGI_1 SRR530835.sra 20982640 19158
## 348 CAU05_478_BGI_2 SRR530836.sra 75322708 78798
## 349 CAU05_478_BGI_2 SRR530837.sra 90188014 93424
## 350 CAU04_5003_BGI_1 SRR530838.sra 55939904 50556
## 351 CAU04_5003_BGI_2 SRR530840.sra 15798530 15734
## 352 CAU04_5003_BGI_2 SRR530841.sra 18499012 18108
## 353 CAU223_H99 SRR671686.sra 12430556 12334
## 354 CAU268_B8 SRR671687.sra 12322140 12770
## 355 CAU272_M14 SRR671688.sra 10879300 12030
## 356 CAU364_B7 SRR671689.sra 9320448 11514
## 357 CAU427_H105W SRR671715.sra 14671396 13626
## 358 CAU532_PHG35 SRR671716.sra 18012100 22058
## 359 CAU308_W117 SRR801200.sra 7924472 9560
## 360 CAU421_CI66 SRR801201.sra 6403484 5286
N = (x$Line)
x$Accession = NULL
fbyN = factor(N, exclude = " ")
x$Line = NULL
abun = aggregate(x, by = list(fbyN), FUN = "mean", na.rm = T)
abun2 = Filter(function(abun) !all(is.na(abun)), abun)
A = (abun2$Group.1)
B = (abun2$Total_Reads)
C = (abun2$Reads_Mapped)
## Percent reads mapped per lane
D = (abun2$Reads_Mapped/abun2$Total_Reads) * 100
abun3 = data.frame(A, B, C, D)
Columns
$A = Lines $B = Total_Reads $C = Reads_Mapped $D = Percent Abundance
print(abun3)
## A B C D
## 1 CAU01_zheng58 209157842 201379 0.09628
## 2 CAU01_Zheng58_BGI_1 38915944 35856 0.09214
## 3 CAU01_Zheng58_BGI_2 60876800 60386 0.09919
## 4 CAU02_chang7-2 217642062 263810 0.12121
## 5 CAU04_5003 206187317 186112 0.09026
## 6 CAU04_5003_BGI_1 55939904 50556 0.09038
## 7 CAU04_5003_BGI_2 17148771 16921 0.09867
## 8 CAU05_478 203426805 203939 0.10025
## 9 CAU05_478_BGI_1 15127382 13720 0.09070
## 10 CAU05_478_BGI_2 82755361 86111 0.10405
## 11 CAU06_zong31 70997500 71069 0.10010
## 12 CAU07_D340 66129891 53985 0.08163
## 13 CAU08_H127 62173255 49150 0.07905
## 14 CAU10_yu87-1 73665576 81314 0.11038
## 15 CAU100_shen5005 12737252 11872 0.09321
## 16 CAU103_807D 16300934 16898 0.10366
## 17 CAU105_1145 27641706 27126 0.09813
## 18 CAU107_D15 53675218 47086 0.08772
## 19 CAU11_longkang11 71101708 65244 0.09176
## 20 CAU112_S22 27845610 23814 0.08552
## 21 CAU114_Q1261 43455832 41566 0.09565
## 22 CAU115_ye52106 50490050 39144 0.07753
## 23 CAU116_1205A 54763896 47004 0.08583
## 24 CAU118_K12 66030204 53400 0.08087
## 25 CAU12_danhuang02 70335690 64104 0.09114
## 26 CAU120_xing230 37385070 34578 0.09249
## 27 CAU125_K22 29202845 28095 0.09621
## 28 CAU129_P007 24565994 19752 0.08040
## 29 CAU131_Yd6 39416476 37072 0.09405
## 30 CAU132_IA5125 34932284 21530 0.06163
## 31 CAU133_liao2202 11502010 9012 0.07835
## 32 CAU134_dai6 31280364 28016 0.08956
## 33 CAU137_W499 34393388 32040 0.09316
## 34 CAU14_shen137 47486836 44720 0.09417
## 35 CAU140_XOP2 44223166 39012 0.08822
## 36 CAU142_D20 38019170 39502 0.10390
## 37 CAU143_hai1134 42870590 40144 0.09364
## 38 CAU144_yu374 32233382 29748 0.09229
## 39 CAU146_dan9064 49368884 46352 0.09389
## 40 CAU147_niu2-1 13537904 13490 0.09965
## 41 CAU148_suwan1611 43960032 45606 0.10374
## 42 CAU149_R017 34029830 31680 0.09309
## 43 CAU15_zheng22 29773608 23152 0.07776
## 44 CAU151_shen977 19930138 17404 0.08733
## 45 CAU156_huangchangb 11487270 10176 0.08859
## 46 CAU16_lv28 57672880 56364 0.09773
## 47 CAU164_K10 19345838 15948 0.08244
## 48 CAU165_ye5237 24707316 20798 0.08418
## 49 CAU166_zheng32 52534964 59814 0.11386
## 50 CAU17_huangC 57496794 56592 0.09843
## 51 CAU173_P167 28673978 27282 0.09515
## 52 CAU174_R31 23611472 21184 0.08972
## 53 CAU178_changK 94898024 71550 0.07540
## 54 CAU18_P138 20583530 16476 0.08004
## 55 CAU180_M131-5 61677804 55892 0.09062
## 56 CAU19_zi330 20203698 15332 0.07589
## 57 CAU191_hai014 29484904 29602 0.10040
## 58 CAU192_ji444 32386756 27488 0.08487
## 59 CAU193_ben7884 26833726 21706 0.08089
## 60 CAU194_huangyesi3 54763730 45388 0.08288
## 61 CAU195_zaC546 26946532 21776 0.08081
## 62 CAU196_ji846 56594520 48646 0.08596
## 63 CAU197_4F1 54015334 53664 0.09935
## 64 CAU198_wenhuang31413 40507588 37282 0.09204
## 65 CAU199_ye515 28398802 27742 0.09769
## 66 CAU20_huangzaosi 191107860 142662 0.07465
## 67 CAU200_hu803 30856650 30090 0.09752
## 68 CAU201_tian77 25134256 24228 0.09639
## 69 CAU202_ye488 34012968 30114 0.08854
## 70 CAU203_chang72 34950426 33198 0.09499
## 71 CAU207_3H2 30423952 25500 0.08382
## 72 CAU208_cheng698-3 45204634 35120 0.07769
## 73 CAU21_tie7922 34600798 32792 0.09477
## 74 CAU210_su75 22677324 20362 0.08979
## 75 CAU211_Beck 24570698 19410 0.07900
## 76 CAU215_P136 21826386 13586 0.06225
## 77 CAU217_dan9046 110652394 79300 0.07167
## 78 CAU223_H99 12430556 12334 0.09922
## 79 CAU224_W64a 28249538 25178 0.08913
## 80 CAU225_A554 22544530 20572 0.09125
## 81 CAU229_xun92-8 25270368 26564 0.10512
## 82 CAU234_H21 8478046 5876 0.06931
## 83 CAU235_shuang741 8072556 6231 0.07719
## 84 CAU236_200B 15653203 11943 0.07630
## 85 CAU237_chong72 8337079 6383 0.07656
## 86 CAU238_Pa91 9208719 8756 0.09508
## 87 CAU239_yu537A 9160202 9000 0.09825
## 88 CAU24_9058 31221240 22574 0.07230
## 89 CAU242_dan3115 38457172 38896 0.10114
## 90 CAU244_zhonghuang64 37820058 31698 0.08381
## 91 CAU247_dong327 19962552 17746 0.08890
## 92 CAU248_698-3 32029636 26694 0.08334
## 93 CAU25_ji853 32828864 31344 0.09548
## 94 CAU251_N138 27867615 22932 0.08229
## 95 CAU254_DM07 22220704 19340 0.08704
## 96 CAU256_B100 14947500 9582 0.06410
## 97 CAU257_B98 60212028 54146 0.08993
## 98 CAU261_lian87 18753222 16086 0.08578
## 99 CAU264_L-1 23719324 22018 0.09283
## 100 CAU268_B8 12322140 12770 0.10363
## 101 CAU27_ye8112_1 71395891 79630 0.11153
## 102 CAU27_ye8112_2 72174463 80324 0.11129
## 103 CAU271_changD 40051050 32926 0.08221
## 104 CAU272_M14 10879300 12030 0.11058
## 105 CAU273_M101 29879810 27370 0.09160
## 106 CAU275_B394 24172980 18620 0.07703
## 107 CAU282_R25 20201754 16759 0.08296
## 108 CAU283_chengzi108 45166164 38330 0.08486
## 109 CAU289_ye107 24702785 18756 0.07593
## 110 CAU29_Maxa 23784756 18664 0.07847
## 111 CAU290_jiutai1 35612130 30134 0.08462
## 112 CAU294_hai9-21 24425646 20866 0.08543
## 113 CAU295_ji533 16621920 13066 0.07861
## 114 CAU297_ye832 11569580 11824 0.10220
## 115 CAU302_B76 11502629 10379 0.09023
## 116 CAU303_NC268 14851894 11625 0.07827
## 117 CAU306_Sg1533 10189611 7179 0.07045
## 118 CAU308_W117 7924472 9560 0.12064
## 119 CAU31_wu126 17207582 16008 0.09303
## 120 CAU310_7327 26323878 20258 0.07696
## 121 CAU316_bao3040 28374614 30016 0.10578
## 122 CAU320_Lx9801 8045754 8369 0.10402
## 123 CAU326_shen135 72490194 67162 0.09265
## 124 CAU33_yi36 19094048 11480 0.06012
## 125 CAU332_baihe43 18218254 16070 0.08821
## 126 CAU34_nan21-3 33345152 40472 0.12137
## 127 CAU345_jiu138-5 49171122 46238 0.09403
## 128 CAU347_ning55 29692712 27624 0.09303
## 129 CAU350_han21 28291238 23204 0.08202
## 130 CAU355_huotanghuang 33904366 29942 0.08831
## 131 CAU357_yu82 24306144 20270 0.08339
## 132 CAU359_CN165 20754496 17664 0.08511
## 133 CAU361_fu8701 20774778 17968 0.08649
## 134 CAU362_De811 15495998 11314 0.07301
## 135 CAU364_B7 9320448 11514 0.12353
## 136 CAU365_shan89 22904378 22028 0.09617
## 137 CAU366_A679 20135748 18924 0.09398
## 138 CAU367_Va26 18801134 15986 0.08503
## 139 CAU370_E28 15454280 12590 0.08147
## 140 CAU372_zhongyin15 13510181 11053 0.08181
## 141 CAU375_zong3 22163646 16210 0.07314
## 142 CAU38_A632 126926214 106827 0.08416
## 143 CAU382_FC-13 22840942 23276 0.10190
## 144 CAU384_ji63 10365382 7087 0.06837
## 145 CAU385_ji434 34082138 27964 0.08205
## 146 CAU386_ji4112 13385360 10801 0.08069
## 147 CAU389_qi205 14425640 12072 0.08368
## 148 CAU39_CM105 35389274 29674 0.08385
## 149 CAU40_B68 13638468 11430 0.08381
## 150 CAU400_P25 32415118 29636 0.09143
## 151 CAU401_R98 26702646 24114 0.09031
## 152 CAU402_qi319 13550715 12116 0.08941
## 153 CAU405_huo17 28841646 26116 0.09055
## 154 CAU409_huangyesi 37093762 30200 0.08142
## 155 CAU41_P39 21084332 11996 0.05690
## 156 CAU411_shen142 21734676 20264 0.09323
## 157 CAU413_siyi 19036904 13878 0.07290
## 158 CAU416_xun971 15462348 15264 0.09872
## 159 CAU42_shangyin110-1 31503948 28720 0.09116
## 160 CAU420_Mo24W 33120802 34348 0.10371
## 161 CAU421_CI66 6403484 5286 0.08255
## 162 CAU422_W182bn 26009118 21176 0.08142
## 163 CAU423_W153R 13300869 12895 0.09695
## 164 CAU425_HP301 12472001 8732 0.07001
## 165 CAU426_H84 17188970 15370 0.08942
## 166 CAU427_H105W 14671396 13626 0.09287
## 167 CAU429_tangsipingtou 38787646 29130 0.07510
## 168 CAU434_cheng18 49272734 41764 0.08476
## 169 CAU436_xinlun5-9 13084908 10194 0.07791
## 170 CAU439_lv45 19311120 18822 0.09747
## 171 CAU446_fengke1 16977582 18986 0.11183
## 172 CAU448_ernan24 51042346 46924 0.09193
## 173 CAU451_78371A 38269034 28448 0.07434
## 174 CAU452_PHT10 27149010 26268 0.09675
## 175 CAU453_PHH93 16415530 11682 0.07116
## 176 CAU454_IBB14 17226950 14212 0.08250
## 177 CAU458_LH149 14163797 13461 0.09504
## 178 CAU46_zhong451 23256652 23364 0.10046
## 179 CAU461_794 19284793 14596 0.07569
## 180 CAU463_PHR32 24227956 17086 0.07052
## 181 CAU465_PHG50 14695312 12188 0.08294
## 182 CAU466_LH51 24417620 18662 0.07643
## 183 CAU468_78010 24898596 28054 0.11267
## 184 CAU47_huotanghuang17 23971790 19828 0.08271
## 185 CAU470_LH39 47102974 35486 0.07534
## 186 CAU471_PHG84 19108702 15300 0.08007
## 187 CAU475_LH57 16830540 13472 0.08004
## 188 CAU476_LH38 16334846 13109 0.08025
## 189 CAU488_807 23807121 21621 0.09082
## 190 CAU489_OH43 34758850 27942 0.08039
## 191 CAU490_PHN11 27764940 23562 0.08486
## 192 CAU491_PHJ70 15360396 14508 0.09445
## 193 CAU492_DJ7 14545486 13486 0.09272
## 194 CAU496_790 15964582 14336 0.08980
## 195 CAU497_PHZ51 24078322 22797 0.09468
## 196 CAU498_PHT60 14620536 10880 0.07442
## 197 CAU501_PHG83 24887488 23948 0.09623
## 198 CAU503_PHJ75 24187540 17402 0.07195
## 199 CAU505_PB80 21949448 21494 0.09793
## 200 CAU510_LH52 13791971 12535 0.09089
## 201 CAU513_PHW52 14638667 10534 0.07196
## 202 CAU514_LH93 17886148 14650 0.08191
## 203 CAU515_PHM57 18103124 18998 0.10494
## 204 CAU517_LH60 11517712 8202 0.07121
## 205 CAU518_PHG71 13590689 8935 0.06574
## 206 CAU520_Q381 20250528 15409 0.07609
## 207 CAU521_MBPM 21247459 11086 0.05218
## 208 CAU522_PHW03 23367036 12281 0.05256
## 209 CAU523_PHW43 14786681 12734 0.08612
## 210 CAU525_LH190 19367306 16752 0.08650
## 211 CAU526_B47 16624604 14944 0.08989
## 212 CAU527_PHV78 33792100 33244 0.09838
## 213 CAU528 26704916 23778 0.08904
## 214 CAU530_PHK76 15586120 14040 0.09008
## 215 CAU531_LH1 28823406 24380 0.08458
## 216 CAU532_PHG35 18012100 22058 0.12246
## 217 CAU534_PHJ31 16875438 19979 0.11839
## 218 CAU535_78002A 12329206 13272 0.10765
## 219 CAU536_792 15532588 14700 0.09464
## 220 CAU537_PHJ40 14269036 11920 0.08354
## 221 CAU538_LH54 29737068 24896 0.08372
## 222 CAU539_FAPW 13815894 10808 0.07823
## 223 CAU541_LH205 16753906 15243 0.09098
## 224 CAU542_LH127 19107152 19752 0.10337
## 225 CAU545_LH194 16181887 14643 0.09049
## 226 CAU546_LH202 12749888 11196 0.08781
## 227 CAU547_LH191_1 10951630 9104 0.08313
## 228 CAU547_LH191_2 23289192 17424 0.07482
## 229 CAU548_LH192_1 10372950 10668 0.10284
## 230 CAU548_LH192_2 14068490 14190 0.10086
## 231 CAU549_RS710 21188898 14329 0.06763
## 232 CAU551_PHW51 18958034 16739 0.08830
## 233 CAU566_PHP85 21451132 22017 0.10264
## 234 CAU572_LH143 45251542 45960 0.10157
## 235 CAU574_207 32057702 27808 0.08674
## 236 CAU575_CR1HT 22266226 20632 0.09266
## 237 CAU576_6103 31176454 28904 0.09271
## 238 CAU577_IB014_1 9392584 7534 0.08021
## 239 CAU577_IB014_2 11433200 8838 0.07730
## 240 CAU578_4676A 22171696 17144 0.07732
## 241 CAU58_B12 55059104 49908 0.09064
## 242 CAU580_PHR36 15165134 13922 0.09180
## 243 CAU581_NS701_1 10179172 9902 0.09728
## 244 CAU581_NS701_2 9626492 9220 0.09578
## 245 CAU582_IB02 20362334 17788 0.08736
## 246 CAU583_IBB15 60631572 56720 0.09355
## 247 CAU584_787 23909270 18418 0.07703
## 248 CAU586_11430 31886404 27100 0.08499
## 249 CAU587_2369 21544254 17806 0.08265
## 250 CAU588_2MA22 17974302 16906 0.09406
## 251 CAU589_87916W_1 10859552 8980 0.08269
## 252 CAU589_87916W_2 8537844 6566 0.07690
## 253 CAU590_MBST 41341714 33934 0.08208
## 254 CAU591_PHN47 27884408 25098 0.09001
## 255 CAU592_NS501 19970744 16752 0.08388
## 256 CAU593_H8431 19612446 17956 0.09155
## 257 CAU594_S8324 22411272 18896 0.08431
## 258 CAU595_CR14 20019684 16952 0.08468
## 259 CAU596_WIL901 18022358 14572 0.08086
## 260 CAU597_WIL903 20377400 16632 0.08162
## 261 CAU598_WIL500 15765472 14348 0.09101
## 262 CAU599_E8501 27138434 21156 0.07796
## 263 CAU601_L135 16290430 14000 0.08594
## 264 CAU604_PHM10 21904365 18297 0.08353
## 265 CAU605_PHN82 26928670 23802 0.08839
## 266 CAU606_PHP60_1 10752754 8746 0.08134
## 267 CAU606_PHP60_2 7504736 4696 0.06257
## 268 CAU607_PHR63 27207243 24864 0.09139
## 269 CAU609_PHV37 39491576 44116 0.11171
## 270 CAU61_ji870 12808268 12284 0.09591
## 271 CAU610_PHW20 20836751 17030 0.08173
## 272 CAU611_W23 15964114 12086 0.07571
## 273 CAU63_fu8521 11713253 8711 0.07437
## 274 CAU631_PHP55 23777761 19820 0.08336
## 275 CAU638_huobai 36451508 28776 0.07894
## 276 CAU68_jiao05 39058972 40972 0.10490
## 277 CAU69_qi410 1352992 1466 0.10835
## 278 CAU73_xiangai3 67539420 60112 0.08900
## 279 CAU74_fusheA 49431430 55224 0.11172
## 280 CAU76_qiong51 56228928 58710 0.10441
## 281 CAU77_DH149 28236574 16102 0.05703
## 282 CAU78_R08 30134172 19306 0.06407
## 283 CAU84_B95 41560921 43091 0.10368
## 284 CAU97_guan17-1 13353680 9144 0.06848
## 285 CAU98_wu125 17059198 14890 0.08728
## 286 Mo17 73289199 59934 0.08178
Statistical Summary
Stats for Percent Abundance
summary(D)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0522 0.0808 0.0883 0.0880 0.0950 0.1240
Average Abundance Across Lines
mean(D)
## [1] 0.08804
Plot showing Percent Reads Mapped per Lane.
hist(D, xlab = "Percent Reads Mapped", ylab = "Jiao Lines", xlim = c(0.03, 0.14),
col = rgb(1, 1, 0, 1/5), main = "CRM2 Abundance")