BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008772.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,195,570 number of mapped reads = 985,383 (82.42%) number of supplementary alignments = 6,330 (0.53%) number of secondary alignments = 0 number of mapped bases = 64,316,336 bp number of sequenced bases = 64,285,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,922 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1302 >>>>>>> ACTG content number of A's = 18,536,323 bp (28.83%) number of C's = 11,542,891 bp (17.96%) number of T's = 19,708,764 bp (30.66%) number of G's = 14,486,734 bp (22.53%) number of N's = 10,975 bp (0.02%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 543,982 number of insertions = 5,557 mapped reads with insertion percentage = 0.56% number of deletions = 18,398 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0208X std coverageData = 0.2262X There is a 1.94% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 6243203 0.025047893461416892 0.38915992825575535 chr2 243199373 6023750 0.024768772738571164 0.2636717839868944 chr3 198022430 4930849 0.024900456983585142 0.1710660953056162 chr4 191154276 3433060 0.017959629634442496 0.14319071569179873 chr5 180915260 3087178 0.017064221116560318 0.13682682324973558 chr6 171115067 3337914 0.01950683863508057 0.15349231269205985 chr7 159138663 3359500 0.021110520452217195 0.24140177300992005 chr8 146364022 4510576 0.030817518802537417 0.24467499431356185 chr9 141213431 1941416 0.01374809737467536 0.18727707614943334 chr10 135534747 3480642 0.025680809364701143 0.3414738847299272 chr11 135006516 3014900 0.022331514724815208 0.21997411685552704 chr12 133851895 2854913 0.021328894895361772 0.15310265621454788 chr13 115169878 1575741 0.013681884771988732 0.12104523653819434 chr14 107349540 2707758 0.025223750376573574 0.16882942646882293 chr15 102531392 1808785 0.0176412800481632 0.14082965093061386 chr16 90354753 1725239 0.019094059169195005 0.1742729392863355 chr17 81195210 1554359 0.01914348149355116 0.18179986603490395 chr18 78077248 1065148 0.013642232881978628 0.3667200450129069 chr19 59128983 1265945 0.021409889630606364 0.26522104115805484 chr20 63025520 1525905 0.02421090694690024 0.16435628113794545 chr21 48129895 605261 0.012575572832643827 0.12475709293828752 chr22 51304566 778965 0.01518315153469966 0.12816878610294438 chrMT 16571 57507 3.4703397501659525 2.553866923682162 chrX 155270560 3258894 0.020988486162476647 0.21535080523324934 chrY 59373566 168928 0.0028451718732878536 0.0875313079655253