BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234029.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 = 1,714,189 number of mapped reads = 1,293,956 (75.49%) number of supplementary alignments = 5,893 (0.34%) number of secondary alignments = 0 number of mapped bases = 85,815,784 bp number of sequenced bases = 85,773,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,790 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7128 >>>>>>> ACTG content number of A's = 24,184,692 bp (28.2%) number of C's = 14,893,218 bp (17.36%) number of T's = 27,571,959 bp (32.15%) number of G's = 19,107,905 bp (22.28%) number of N's = 15,899 bp (0.02%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 705,184 number of insertions = 6,773 mapped reads with insertion percentage = 0.52% number of deletions = 23,772 mapped reads with deletion percentage = 1.82% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2553X There is a 2.47% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6268067 0.02514764847867721 0.3619056281498194 chr2 243199373 7289056 0.02997152463875801 0.28808164945993003 chr3 198022430 6364180 0.03213868247147558 0.19606940718714005 chr4 191154276 3658700 0.01914003744284538 0.162395552518424 chr5 180915260 6411577 0.03543966937891253 0.2065303854731468 chr6 171115067 4458493 0.026055525548781745 0.19708170203945657 chr7 159138663 5480923 0.03444117788019873 0.34857653623061613 chr8 146364022 4127610 0.028200987808329015 0.4230786419888376 chr9 141213431 4036093 0.028581509360819934 0.23924034836013555 chr10 135534747 4452819 0.03285370798677921 0.2453049481206278 chr11 135006516 4284071 0.031732327645578234 0.230912817542858 chr12 133851895 3810966 0.02847151323483317 0.1862865476509614 chr13 115169878 3373394 0.029290592805872383 0.18728990391165545 chr14 107349540 3060326 0.028508049498861383 0.19516447070393306 chr15 102531392 2530682 0.02468202128768524 0.17543781689911453 chr16 90354753 2496107 0.02762563027536581 0.196045676341472 chr17 81195210 1583887 0.019507148266504883 0.15538141947101183 chr18 78077248 2629126 0.03367339484096571 0.4548986301274745 chr19 59128983 1473335 0.024917306627783537 0.2686067299411701 chr20 63025520 1528368 0.024249986354733764 0.17845134086090536 chr21 48129895 1317272 0.027369101885636776 0.19068648313354966 chr22 51304566 942807 0.018376668462608183 0.14734054871200475 chrMT 16571 51309 3.096312835676785 2.5691630516127444 chrX 155270560 3986098 0.02567194965999994 0.18799498376190868 chrY 59373566 200518 0.0033772268285182667 0.0912506892241844