BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013199.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 = 1,612,502 number of mapped reads = 1,314,664 (81.53%) number of supplementary alignments = 9,736 (0.6%) number of secondary alignments = 0 number of mapped bases = 84,608,109 bp number of sequenced bases = 84,561,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,844 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8312 >>>>>>> ACTG content number of A's = 22,927,850 bp (27.11%) number of C's = 15,101,613 bp (17.86%) number of T's = 27,490,714 bp (32.51%) number of G's = 19,039,866 bp (22.52%) number of N's = 1,168 bp (0%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 694,963 number of insertions = 5,816 mapped reads with insertion percentage = 0.44% number of deletions = 27,282 mapped reads with deletion percentage = 2.05% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2568X There is a 2.19% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.08% 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 5315894 0.02132750553909352 0.35301543691338855 chr2 243199373 9322627 0.03833326905822245 0.3450722769652062 chr3 198022430 6662470 0.03364502698002443 0.22161489770444495 chr4 191154276 3849114 0.02013616478032644 0.1763198377863376 chr5 180915260 3522454 0.019470187313110017 0.1704028724898148 chr6 171115067 3893116 0.022751450636430515 0.2514723982493103 chr7 159138663 4288724 0.026949604320855705 0.29921353850862425 chr8 146364022 4750012 0.032453412628958775 0.29076780167363475 chr9 141213431 2380522 0.016857617459914275 0.22604847378541704 chr10 135534747 5534357 0.04083349194579601 0.3099224619841488 chr11 135006516 3059846 0.022664431989341906 0.20785277308418088 chr12 133851895 5650979 0.042218147154360425 0.2497321704344727 chr13 115169878 2786255 0.0241925670877241 0.1867255448184646 chr14 107349540 2666457 0.024839016543526875 0.19464933779441151 chr15 102531392 2242173 0.021868161118889326 0.17843738231993897 chr16 90354753 3388408 0.037501159457543974 0.24006643268806852 chr17 81195210 2444565 0.030107256327066585 0.2204965139666128 chr18 78077248 1748566 0.022395333401095285 0.36599810689935447 chr19 59128983 1541314 0.026066979707734868 0.29687507227321225 chr20 63025520 1792919 0.028447508247452777 0.20225417782274596 chr21 48129895 1878769 0.039035385387813544 0.24746928070125748 chr22 51304566 796456 0.015524076356088852 0.14761841339989618 chrMT 16571 26409 1.593687767787098 1.7378006450337489 chrX 155270560 4871867 0.031376630573110575 0.2257479544095759 chrY 59373566 193836 0.0032646851630909286 0.08100677620544022