BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716730.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,471,859 number of mapped reads = 2,836,580 (81.7%) number of supplementary alignments = 11,610 (0.33%) number of secondary alignments = 0 number of mapped bases = 162,020,712 bp number of sequenced bases = 161,969,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,636 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8831 >>>>>>> ACTG content number of A's = 39,839,590 bp (24.6%) number of C's = 32,001,087 bp (19.76%) number of T's = 52,904,868 bp (32.66%) number of G's = 37,221,599 bp (22.98%) number of N's = 2,457 bp (0%) GC percentage = 42.74% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 850,412 number of insertions = 11,013 mapped reads with insertion percentage = 0.39% number of deletions = 32,177 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.62% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.3902X There is a 4.43% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12763392 0.051207061987620886 0.5285637503579381 chr2 243199373 13797356 0.056732695606086125 0.6447813916660292 chr3 198022430 10905812 0.05507361969045628 0.2734133638239332 chr4 191154276 10206178 0.053392360419915484 0.31901460888272204 chr5 180915260 9825720 0.05431117308733382 0.2690625591911107 chr6 171115067 9178846 0.05364136636781377 0.32434878363948266 chr7 159138663 9053602 0.05689127851979 0.5431400543920519 chr8 146364022 8038642 0.054922254049564176 0.35637583456444466 chr9 141213431 6655590 0.047131423355898774 0.3126238961198755 chr10 135534747 7642934 0.05639095633535214 0.44450346835527804 chr11 135006516 7210842 0.05341106647030281 0.3354134037884656 chr12 133851895 7526212 0.05622790771845255 0.2792377319770012 chr13 115169878 5074808 0.044063674357630214 0.2437989870324306 chr14 107349540 4982225 0.04641123753301598 0.2631066176834538 chr15 102531392 4746128 0.04628951102117096 0.25410801943510647 chr16 90354753 4805427 0.05318399796854074 0.3029030578498304 chr17 81195210 4652677 0.05730235810708538 0.30603085286913617 chr18 78077248 4253906 0.05448329838674642 0.5704074630289607 chr19 59128983 3507752 0.05932373299909454 0.4441662275109416 chr20 63025520 3383237 0.053680429768766684 0.27823251194798454 chr21 48129895 2100213 0.04363635117009917 0.2757109788223311 chr22 51304566 2019032 0.03935384620542351 0.2307198778708969 chrMT 16571 29600 1.7862530927523987 1.7167612630066944 chrX 155270560 9166062 0.059032839193727385 0.3153204565505618 chrY 59373566 494519 0.008328942209736906 0.21553931105891888