BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618657.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 40,992,774 number of mapped reads = 38,957,036 (95.03%) number of supplementary alignments = 113,806 (0.28%) number of secondary alignments = 0 number of mapped bases = 3,803,791,547 bp number of sequenced bases = 3,801,192,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,774,021 duplication rate = 30.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3432 >>>>>>> ACTG content number of A's = 1,042,479,660 bp (27.43%) number of C's = 833,692,951 bp (21.93%) number of T's = 1,059,654,378 bp (27.88%) number of G's = 827,566,547 bp (21.77%) number of N's = 37,798,702 bp (0.99%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0197 number of mismatches = 73,844,774 number of insertions = 685,712 mapped reads with insertion percentage = 1.74% number of deletions = 1,890,984 mapped reads with deletion percentage = 4.74% homopolymer indels = 53.36% >>>>>>> Coverage mean coverageData = 1.2287X std coverageData = 4.5172X There is a 24.64% of reference with a coverageData >= 1X There is a 16.86% of reference with a coverageData >= 2X There is a 12.61% of reference with a coverageData >= 3X There is a 9.83% of reference with a coverageData >= 4X There is a 7.87% of reference with a coverageData >= 5X There is a 6.41% of reference with a coverageData >= 6X There is a 5.3% of reference with a coverageData >= 7X There is a 4.44% of reference with a coverageData >= 8X There is a 3.76% of reference with a coverageData >= 9X There is a 3.22% of reference with a coverageData >= 10X There is a 2.78% of reference with a coverageData >= 11X There is a 2.41% of reference with a coverageData >= 12X There is a 2.11% of reference with a coverageData >= 13X There is a 1.85% of reference with a coverageData >= 14X There is a 1.64% of reference with a coverageData >= 15X There is a 1.45% of reference with a coverageData >= 16X There is a 1.29% of reference with a coverageData >= 17X There is a 1.15% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 0.93% of reference with a coverageData >= 20X There is a 0.84% of reference with a coverageData >= 21X There is a 0.76% of reference with a coverageData >= 22X There is a 0.69% of reference with a coverageData >= 23X There is a 0.63% of reference with a coverageData >= 24X There is a 0.57% of reference with a coverageData >= 25X There is a 0.52% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.43% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.37% of reference with a coverageData >= 30X There is a 0.34% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.29% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 338833820 1.3594101336261064 5.403648236144858 chr2 243199373 316676933 1.3021289039260804 4.884368554164597 chr3 198022430 248579050 1.2553075426859472 3.999542869487601 chr4 191154276 194562569 1.0178300641310267 3.8748009776093624 chr5 180915260 215359799 1.1903904568359795 3.84972445141729 chr6 171115067 204915464 1.1975302209945078 3.987715873521221 chr7 159138663 190933708 1.1997945967410824 4.269473306017202 chr8 146364022 188469868 1.2876789351962465 4.28778253464453 chr9 141213431 163581604 1.158399755898573 4.623016305163603 chr10 135534747 192408580 1.4196254780333193 4.486954440691762 chr11 135006516 192643020 1.4269164608321572 5.3300833785881245 chr12 133851895 165843622 1.2390083980506963 4.067149746300735 chr13 115169878 101062167 0.8775052014902717 3.2134611713044423 chr14 107349540 114232497 1.0641172472653353 3.810679767880938 chr15 102531392 124238190 1.2117088003642826 4.180726735663982 chr16 90354753 129248209 1.4304527953277677 6.010086507119111 chr17 81195210 121858655 1.5008108852726658 4.984331774820729 chr18 78077248 93776537 1.2010738006544492 5.431397045565 chr19 59128983 78980263 1.3357284193438606 5.106943486764357 chr20 63025520 106012982 1.6820643764621062 5.213695204175894 chr21 48129895 47513291 0.9871887524375442 5.899874441018721 chr22 51304566 67737683 1.3203051556853633 4.827849361695641 chrMT 16571 4495 0.27125701526763624 1.1958945076004588 chrX 155270560 200640088 1.2921965889734668 4.158639147109944 chrY 59373566 5678453 0.0956394130007283 1.7217226064012074