BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525081.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 = 1,908,284 number of mapped reads = 1,502,869 (78.75%) number of supplementary alignments = 6,622 (0.35%) number of secondary alignments = 0 number of mapped bases = 89,095,576 bp number of sequenced bases = 89,066,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,699 duplication rate = 3.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9237 >>>>>>> ACTG content number of A's = 23,514,256 bp (26.4%) number of C's = 16,783,273 bp (18.84%) number of T's = 28,077,883 bp (31.52%) number of G's = 20,681,748 bp (23.22%) number of N's = 9,568 bp (0.01%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 422,832 number of insertions = 6,640 mapped reads with insertion percentage = 0.44% number of deletions = 17,665 mapped reads with deletion percentage = 1.17% homopolymer indels = 40.77% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.2636X There is a 2.53% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 7178771 0.028801416707403108 0.458262157150395 chr2 243199373 7573670 0.031141815484861467 0.3264250660927482 chr3 198022430 5893779 0.029763188947837877 0.19235360037638985 chr4 191154276 5770237 0.030186282623361246 0.2221324319787824 chr5 180915260 5387732 0.029780417638622634 0.19151092934056838 chr6 171115067 5086469 0.029725430315262653 0.20710877978791814 chr7 159138663 4895495 0.030762448971938392 0.30401491408924075 chr8 146364022 4495366 0.030713599821682955 0.2871189040329305 chr9 141213431 3731125 0.026421884756840163 0.22108079226638228 chr10 135534747 4289468 0.03164847461588577 0.3072950802407285 chr11 135006516 4047695 0.029981478819881554 0.22400278529012016 chr12 133851895 3988873 0.029800646453305723 0.19487089048417364 chr13 115169878 2783254 0.024166509927187732 0.17188254929412156 chr14 107349540 2673155 0.024901410849082352 0.17837753604825365 chr15 102531392 2619162 0.025544976508267828 0.17819410145723108 chr16 90354753 2630405 0.029111971563908764 0.20482810144444633 chr17 81195210 2369584 0.029183790521632988 0.1985238714034554 chr18 78077248 2382957 0.03052050451368368 0.34737983238606085 chr19 59128983 1798744 0.030420682188969834 0.332203454604963 chr20 63025520 1907904 0.03027192794283966 0.1994080979670674 chr21 48129895 1182707 0.02457323042154985 0.20108127539611473 chr22 51304566 1075897 0.020970784549663668 0.1611227834888955 chrMT 16571 15844 0.9561281757286826 1.0703042772684555 chrX 155270560 5010111 0.03226697321114833 0.214729076892646 chrY 59373566 307172 0.005173548107250287 0.17246071297038693