BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008802.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 = 1,262,778 number of mapped reads = 1,154,571 (91.43%) number of supplementary alignments = 13,837 (1.1%) number of secondary alignments = 0 number of mapped bases = 77,777,604 bp number of sequenced bases = 77,740,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,674 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2968 >>>>>>> ACTG content number of A's = 21,220,443 bp (27.3%) number of C's = 15,250,463 bp (19.62%) number of T's = 23,683,619 bp (30.46%) number of G's = 17,477,990 bp (22.48%) number of N's = 108,068 bp (0.14%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 630,642 number of insertions = 5,464 mapped reads with insertion percentage = 0.47% number of deletions = 21,124 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2349X There is a 1.99% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 5719842 0.022948155463171343 0.32599939333898603 chr2 243199373 5523992 0.02271384145385934 0.32218665852901046 chr3 198022430 6620542 0.033433293390046775 0.22506562007236897 chr4 191154276 4913946 0.02570670195209235 0.19883803704008493 chr5 180915260 4371998 0.02416599904286681 0.18975394393646466 chr6 171115067 5910641 0.034541908574304565 0.24597643369986077 chr7 159138663 3772936 0.023708481200448443 0.25010941075640486 chr8 146364022 3693287 0.02523357140322367 0.2345761080830215 chr9 141213431 2239226 0.015857032749243237 0.16911508094637065 chr10 135534747 3549605 0.026189630914351433 0.25800484289668 chr11 135006516 3283744 0.024322855646463762 0.20585404598041834 chr12 133851895 3552783 0.02654264252291684 0.20053133767189568 chr13 115169878 1661091 0.014422963962851467 0.14761584604713676 chr14 107349540 2457096 0.022888742699782413 0.1892346607222108 chr15 102531392 2829964 0.027600951716328984 0.20501141285089933 chr16 90354753 2188703 0.02422344068606994 0.19420202885984003 chr17 81195210 3145026 0.03873413222282447 0.24607151439155336 chr18 78077248 1851956 0.023719534786881834 0.2508354317245189 chr19 59128983 2210526 0.03738481346787243 0.31036896867893354 chr20 63025520 1776760 0.028191120041532382 0.2079876361095409 chr21 48129895 819225 0.017021125851199134 0.1616291829639411 chr22 51304566 1074299 0.02093963722449187 0.17749557527141951 chrMT 16571 7874 0.4751674612274455 0.8955576923628681 chrX 155270560 4419503 0.02846323862037981 0.20949701525470013 chrY 59373566 183039 0.0030828365606337337 0.06817765606296668