BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472536.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 = 18,741,172 number of mapped reads = 18,491,038 (98.67%) number of supplementary alignments = 66,834 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,273,791 number of mapped paired reads (second in pair) = 9,217,247 number of mapped paired reads (both in pair) = 18,366,748 number of mapped paired reads (singletons) = 124,290 number of mapped bases = 1,820,653,199 bp number of sequenced bases = 1,820,425,394 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,098,015 duplication rate = 45.53% >>>>>>> Insert size mean insert size = 23,800.5447 std insert size = 1,490,673.1851 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 54.7693 >>>>>>> ACTG content number of A's = 509,115,410 bp (27.97%) number of C's = 404,032,488 bp (22.19%) number of T's = 506,116,102 bp (27.8%) number of G's = 400,881,364 bp (22.02%) number of N's = 280,030 bp (0.02%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 10,992,276 number of insertions = 95,472 mapped reads with insertion percentage = 0.51% number of deletions = 90,634 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.5881X std coverageData = 22.8472X There is a 5.73% of reference with a coverageData >= 1X There is a 2.58% of reference with a coverageData >= 2X There is a 1.15% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% 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 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% 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 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% 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 0.19% 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 0.18% of reference with a coverageData >= 37X There is a 0.18% 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 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% 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 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% 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 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 180635723 0.7247152375199097 24.792675399208463 chr2 243199373 106332252 0.43722255813546035 18.589902986696266 chr3 198022430 258811912 1.3069828099776373 39.06877326293574 chr4 191154276 60754492 0.31782962574167056 11.299804372413645 chr5 180915260 71921157 0.3975405778373809 13.304284808669827 chr6 171115067 139507603 0.8152853249328418 28.03265612276871 chr7 159138663 82174077 0.5163677729276889 21.461629020853277 chr8 146364022 106064467 0.7246621509212148 36.21796316759994 chr9 141213431 87061249 0.6165224397104266 16.83839543337298 chr10 135534747 44995920 0.3319880768287412 14.197810862698741 chr11 135006516 86849805 0.6433008389017313 22.133572877458228 chr12 133851895 96243658 0.7190309707606306 28.9333120452192 chr13 115169878 36347844 0.3156020014191558 12.651922193636201 chr14 107349540 49310364 0.45934397110597774 17.680308752082592 chr15 102531392 36685522 0.3577979512850074 11.754436812198557 chr16 90354753 71151010 0.7874628355190125 24.183371368723567 chr17 81195210 61693888 0.75982176781118 24.385807913480896 chr18 78077248 45449383 0.5821079016514517 30.88721343605041 chr19 59128983 23154664 0.39159584395354813 8.972005223002476 chr20 63025520 47925793 0.7604188430337425 25.52860421230894 chr21 48129895 6108758 0.1269223213555733 5.197040463227684 chr22 51304566 11162424 0.21757174595337186 5.352595470593897 chrMT 16571 3620 0.21845392553255688 0.6307199475522522 chrX 155270560 107722252 0.6937712596644207 23.259859192895878 chrY 59373566 2585362 0.04354399060349517 1.1983388219524873