BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234145.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 = 2,165,844 number of mapped reads = 817,784 (37.76%) number of supplementary alignments = 8,054 (0.37%) number of secondary alignments = 0 number of mapped bases = 53,426,138 bp number of sequenced bases = 53,402,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,579 duplication rate = 10.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7352 >>>>>>> ACTG content number of A's = 15,182,563 bp (28.43%) number of C's = 9,393,705 bp (17.59%) number of T's = 17,495,357 bp (32.76%) number of G's = 11,322,121 bp (21.2%) number of N's = 8,440 bp (0.02%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 412,163 number of insertions = 5,221 mapped reads with insertion percentage = 0.63% number of deletions = 13,539 mapped reads with deletion percentage = 1.63% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.2811X There is a 0.83% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 4791559 0.01922385982741443 0.3665617638747338 chr2 243199373 4911824 0.02019669680645106 0.29215654729715274 chr3 198022430 3401978 0.017179760898803232 0.24342294271616 chr4 191154276 3837870 0.020077343182215813 0.2692590349931572 chr5 180915260 3658386 0.020221544606021626 0.27248968554799247 chr6 171115067 3600128 0.021039222688671828 0.2765781548919902 chr7 159138663 2543013 0.01597985651041947 0.27144657256855725 chr8 146364022 2953082 0.020176283485841898 0.4742093228985579 chr9 141213431 2312875 0.01637857662420227 0.25480415979910387 chr10 135534747 2268226 0.016735383731523844 0.26499313628011484 chr11 135006516 2604733 0.019293387291025272 0.2703117536028676 chr12 133851895 3051047 0.02279420100851019 0.29051108030065464 chr13 115169878 1643796 0.014272794488850635 0.24255958541551872 chr14 107349540 1714054 0.01596703628166455 0.24406392287804135 chr15 102531392 1322812 0.012901531659689162 0.20756899972461915 chr16 90354753 1060560 0.011737733376350439 0.19505335602234722 chr17 81195210 1063678 0.013100255544631265 0.20853110448517576 chr18 78077248 1343438 0.017206523467630415 0.3490302068866244 chr19 59128983 806448 0.013638793685999977 0.2724702568796009 chr20 63025520 899635 0.014274138475969735 0.2121970344322272 chr21 48129895 580635 0.012063915784565912 0.20204447593362612 chr22 51304566 441541 0.008606271028586422 0.16808063610685092 chrMT 16571 20402 1.2311870134572447 1.9329574667635423 chrX 155270560 2446488 0.015756290181474196 0.23489313364343478 chrY 59373566 147930 0.002491512805547169 0.08364970443622832