BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716838.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 = 3,816,323 number of mapped reads = 3,199,435 (83.84%) number of supplementary alignments = 20,304 (0.53%) number of secondary alignments = 0 number of mapped bases = 185,419,052 bp number of sequenced bases = 185,368,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,631 duplication rate = 5.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1603 >>>>>>> ACTG content number of A's = 47,694,947 bp (25.73%) number of C's = 35,694,586 bp (19.26%) number of T's = 58,388,172 bp (31.5%) number of G's = 43,589,521 bp (23.52%) number of N's = 1,332 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 915,969 number of insertions = 11,871 mapped reads with insertion percentage = 0.37% number of deletions = 32,016 mapped reads with deletion percentage = 0.99% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.4803X There is a 4.68% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 23294291 0.09345730376334749 0.7432020539224147 chr2 243199373 17350383 0.07134221929100122 0.696320124022339 chr3 198022430 12562540 0.06343998505623832 0.3104242387046537 chr4 191154276 8318148 0.04351536452158674 0.31508136096113243 chr5 180915260 14420591 0.07970909142766619 0.3527310328994491 chr6 171115067 4710584 0.027528750580450054 0.24154472528549975 chr7 159138663 13327644 0.08374862367669886 0.8657841730581549 chr8 146364022 8749326 0.05977784622507846 0.43318843853833655 chr9 141213431 5463958 0.03869290591770977 0.3508046268108039 chr10 135534747 8906532 0.06571401206806399 0.4241703389312202 chr11 135006516 8181765 0.060602741574340015 0.4722349360544594 chr12 133851895 7412754 0.055380269364135634 0.294442092834209 chr13 115169878 5643363 0.049000338439188065 0.27502294993553056 chr14 107349540 4304595 0.040098867680290015 0.27165466287182466 chr15 102531392 8574573 0.08362875830262793 0.3647196193072999 chr16 90354753 5868120 0.06494533829338231 0.3420538516947104 chr17 81195210 6820577 0.08400220899730415 0.4172694493789597 chr18 78077248 3647110 0.04671155930086061 0.8050873505291783 chr19 59128983 1922466 0.032513090915160844 0.5404889221181396 chr20 63025520 4551766 0.07222099873194224 0.34178097842473476 chr21 48129895 1798053 0.03735834038283275 0.27011772150841834 chr22 51304566 1966866 0.038337055614114345 0.24216136808158722 chrMT 16571 169320 10.21785046164987 6.788095533066551 chrX 155270560 7008963 0.04514032151362113 0.31360126105425923 chrY 59373566 444764 0.0074909430233649765 0.1837748980335511