BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927005.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,924,556 number of mapped reads = 11,663,884 (97.81%) number of supplementary alignments = 247,439 (2.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,851,785 number of mapped paired reads (second in pair) = 5,812,099 number of mapped paired reads (both in pair) = 11,495,768 number of mapped paired reads (singletons) = 168,116 number of mapped bases = 1,062,252,633 bp number of sequenced bases = 1,061,449,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 695,530 duplication rate = 4.84% >>>>>>> Insert size mean insert size = 220,842.1099 std insert size = 4,583,914.0703 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 53.0092 >>>>>>> ACTG content number of A's = 306,042,593 bp (28.83%) number of C's = 203,376,845 bp (19.16%) number of T's = 311,589,129 bp (29.36%) number of G's = 240,239,448 bp (22.63%) number of N's = 201,109 bp (0.02%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 10,177,577 number of insertions = 179,818 mapped reads with insertion percentage = 1.52% number of deletions = 551,864 mapped reads with deletion percentage = 4.61% homopolymer indels = 52.26% >>>>>>> Coverage mean coverageData = 0.3431X std coverageData = 1.4344X There is a 20.16% of reference with a coverageData >= 1X There is a 7.84% of reference with a coverageData >= 2X There is a 3.08% of reference with a coverageData >= 3X There is a 1.37% of reference with a coverageData >= 4X There is a 0.64% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 86693835 0.34781792980969145 1.8145575909648293 chr2 243199373 91967760 0.37815788283302854 2.365870803346859 chr3 198022430 71113579 0.3591188079047409 0.8745167469740063 chr4 191154276 71321368 0.3731089332262701 1.2585478423368133 chr5 180915260 64022066 0.3538787496422358 0.8588903395780372 chr6 171115067 61403151 0.3588412877750853 1.0526114946073852 chr7 159138663 53980907 0.3392067394709732 1.167904274628228 chr8 146364022 52228831 0.35684200451938936 1.0104691149670668 chr9 141213431 48220198 0.3414703379029152 1.7778390644421325 chr10 135534747 53222118 0.39268246097806936 2.737901790524691 chr11 135006516 49636906 0.3676630393158209 1.1139968858383424 chr12 133851895 46995338 0.3510995343024467 0.879066516657559 chr13 115169878 32471283 0.28194249715190284 0.7656842367014494 chr14 107349540 31992714 0.29802376423783467 0.8129292557733366 chr15 102531392 31115012 0.3034681514906186 0.82217861460846 chr16 90354753 34706841 0.38411749075336415 1.8379160464203517 chr17 81195210 25620676 0.3155441805003029 1.0322177390282536 chr18 78077248 28157719 0.36063923513287766 1.596828241386867 chr19 59128983 16060535 0.2716186578077962 1.265332207085737 chr20 63025520 23960801 0.3801761730803649 0.942752570919557 chr21 48129895 12926200 0.26856904632765144 1.1990867227952864 chr22 51304566 11968778 0.23328874860767754 0.7338388472349788 chrMT 16571 21541 1.2999215496952508 1.9037009720532243 chrX 155270560 60527272 0.3898180827067282 1.0108650834377566 chrY 59373566 1917204 0.03229053144626685 1.2714422039916282