BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472492.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,448,592 number of mapped reads = 17,117,552 (98.1%) number of supplementary alignments = 80,713 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,619,615 number of mapped paired reads (second in pair) = 8,497,937 number of mapped paired reads (both in pair) = 16,938,096 number of mapped paired reads (singletons) = 179,456 number of mapped bases = 1,685,460,207 bp number of sequenced bases = 1,685,225,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,947,850 duplication rate = 44.92% >>>>>>> Insert size mean insert size = 33,242.6594 std insert size = 1,782,040.3592 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 54.85 >>>>>>> ACTG content number of A's = 472,867,373 bp (28.06%) number of C's = 371,559,055 bp (22.05%) number of T's = 470,694,536 bp (27.93%) number of G's = 369,845,085 bp (21.95%) number of N's = 259,271 bp (0.02%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 11,077,378 number of insertions = 96,129 mapped reads with insertion percentage = 0.55% number of deletions = 97,604 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.5445X std coverageData = 20.8234X There is a 5.43% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 1.15% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% 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 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 161899082 0.6495433445680362 27.059754056679072 chr2 243199373 114274317 0.4698791595979978 21.729154858454805 chr3 198022430 162938333 0.8228276614926905 19.22869577286921 chr4 191154276 81243911 0.4250174921538245 19.95750291812929 chr5 180915260 116301067 0.6428482981479837 26.23929611637008 chr6 171115067 112684691 0.6585316709720249 22.309185652444516 chr7 159138663 68964606 0.4333617280673019 13.024894262084674 chr8 146364022 83053570 0.5674452564579019 21.125911350306573 chr9 141213431 118048835 0.8359603910480725 26.9001446681139 chr10 135534747 62925557 0.46427619774875883 22.459834227311426 chr11 135006516 77994641 0.5777101973359567 26.49909259596456 chr12 133851895 88566829 0.6616778118830517 20.223967645974117 chr13 115169878 40246108 0.3494499490569921 19.918982050743196 chr14 107349540 38297757 0.3567575324496034 13.393909580550345 chr15 102531392 44752663 0.43647766920008263 17.108795354581055 chr16 90354753 57738728 0.6390225868914721 19.058252766456025 chr17 81195210 59373895 0.73124873991951 17.554984299927224 chr18 78077248 27349932 0.3502932377944469 13.597897505711169 chr19 59128983 24554610 0.41527198260792003 14.975759678742147 chr20 63025520 34395321 0.5457364096321617 18.5609009974542 chr21 48129895 7253171 0.15069991322441073 6.818860785659121 chr22 51304566 9313205 0.1815278000792366 5.144787143739268 chrMT 16571 4290 0.2588860056725605 0.9023566864743737 chrX 155270560 90622486 0.5836424239083056 20.835598783485775 chrY 59373566 2662602 0.044844906233188014 1.7680075442663177