BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504617.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 296,464,732 number of mapped reads = 281,303,115 (94.89%) number of supplementary alignments = 3,056,532 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 141,097,767 number of mapped paired reads (second in pair) = 140,205,348 number of mapped paired reads (both in pair) = 277,130,178 number of mapped paired reads (singletons) = 4,172,937 number of mapped bases = 27,118,471,460 bp number of sequenced bases = 27,093,094,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,264,341 duplication rate = 18.13% >>>>>>> Insert size mean insert size = 115,612.165 std insert size = 3,204,011.8528 median insert size = 337 >>>>>>> Mapping quality mean mapping quality = 52.3442 >>>>>>> ACTG content number of A's = 7,222,822,796 bp (26.66%) number of C's = 6,279,493,800 bp (23.18%) number of T's = 7,299,121,706 bp (26.94%) number of G's = 6,287,536,427 bp (23.21%) number of N's = 4,119,540 bp (0.02%) GC percentage = 46.38% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 271,016,325 number of insertions = 8,255,629 mapped reads with insertion percentage = 2.71% number of deletions = 7,702,597 mapped reads with deletion percentage = 2.55% homopolymer indels = 34.56% >>>>>>> Coverage mean coverageData = 8.7601X std coverageData = 216.1613X There is a 82.98% of reference with a coverageData >= 1X There is a 74.07% of reference with a coverageData >= 2X There is a 65.64% of reference with a coverageData >= 3X There is a 58.18% of reference with a coverageData >= 4X There is a 51.61% of reference with a coverageData >= 5X There is a 45.86% of reference with a coverageData >= 6X There is a 40.79% of reference with a coverageData >= 7X There is a 36.31% of reference with a coverageData >= 8X There is a 32.35% of reference with a coverageData >= 9X There is a 28.82% of reference with a coverageData >= 10X There is a 25.68% of reference with a coverageData >= 11X There is a 22.87% of reference with a coverageData >= 12X There is a 20.37% of reference with a coverageData >= 13X There is a 18.15% of reference with a coverageData >= 14X There is a 16.16% of reference with a coverageData >= 15X There is a 14.39% of reference with a coverageData >= 16X There is a 12.82% of reference with a coverageData >= 17X There is a 11.42% of reference with a coverageData >= 18X There is a 10.18% of reference with a coverageData >= 19X There is a 9.08% of reference with a coverageData >= 20X There is a 8.1% of reference with a coverageData >= 21X There is a 7.24% of reference with a coverageData >= 22X There is a 6.47% of reference with a coverageData >= 23X There is a 5.79% of reference with a coverageData >= 24X There is a 5.19% of reference with a coverageData >= 25X There is a 4.65% of reference with a coverageData >= 26X There is a 4.18% of reference with a coverageData >= 27X There is a 3.76% of reference with a coverageData >= 28X There is a 3.39% of reference with a coverageData >= 29X There is a 3.07% of reference with a coverageData >= 30X There is a 2.78% of reference with a coverageData >= 31X There is a 2.52% of reference with a coverageData >= 32X There is a 2.29% of reference with a coverageData >= 33X There is a 2.09% of reference with a coverageData >= 34X There is a 1.91% of reference with a coverageData >= 35X There is a 1.75% of reference with a coverageData >= 36X There is a 1.61% of reference with a coverageData >= 37X There is a 1.48% of reference with a coverageData >= 38X There is a 1.37% of reference with a coverageData >= 39X There is a 1.27% of reference with a coverageData >= 40X There is a 1.18% of reference with a coverageData >= 41X There is a 1.1% of reference with a coverageData >= 42X There is a 1.03% of reference with a coverageData >= 43X There is a 0.96% of reference with a coverageData >= 44X There is a 0.91% of reference with a coverageData >= 45X There is a 0.85% of reference with a coverageData >= 46X There is a 0.8% of reference with a coverageData >= 47X There is a 0.76% of reference with a coverageData >= 48X There is a 0.72% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2091277191 8.390258698693472 61.47264326870753 chr2 243199373 2149760560 8.839498776174887 229.56756348631555 chr3 198022430 1439299506 7.268366043180058 19.670576312910942 chr4 191154276 2027767661 10.608016223503157 606.7651157378913 chr5 180915260 1403435176 7.7574173455572515 32.686776825989305 chr6 171115067 1155141293 6.750669670719295 30.27733180433369 chr7 159138663 1333089500 8.376905240180383 32.58577832715793 chr8 146364022 1266907513 8.655867034044746 151.11214375033038 chr9 141213431 990610175 7.014985529244736 64.76072936108268 chr10 135534747 1777356389 13.113658514447222 459.8471856778523 chr11 135006516 1163359703 8.617063364556419 27.270895262866965 chr12 133851895 1082243605 8.085381271591261 16.58927400249291 chr13 115169878 600415541 5.213303612251807 13.301843002217298 chr14 107349540 723374092 6.738492703368827 29.37619735625305 chr15 102531392 792448911 7.728841826315984 14.120403946034866 chr16 90354753 1226135561 13.57023864588507 177.66818033720838 chr17 81195210 940412275 11.58211518881471 64.27782341277883 chr18 78077248 616157683 7.891641915965071 250.1262768800411 chr19 59128983 919135190 15.544579719898108 37.303677175682814 chr20 63025520 696924018 11.057806710678468 143.63171269321953 chr21 48129895 452530036 9.402265182585584 192.32717602691497 chr22 51304566 507834780 9.898432431920387 29.022009129292588 chrMT 16571 10525596 635.181702975077 281.62364845099995 chrX 155270560 1318249805 8.490017714884264 18.662006635968737 chrY 59373566 434079700 7.310992572014286 514.210899957962