BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524568.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 = 5,206,067 number of mapped reads = 4,775,836 (91.74%) number of supplementary alignments = 18,762 (0.36%) number of secondary alignments = 0 number of mapped bases = 278,938,118 bp number of sequenced bases = 278,853,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 386,862 duplication rate = 5.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0576 >>>>>>> ACTG content number of A's = 66,854,802 bp (23.97%) number of C's = 50,019,898 bp (17.94%) number of T's = 91,575,584 bp (32.84%) number of G's = 70,399,254 bp (25.25%) number of N's = 3,851 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,393,243 number of insertions = 15,127 mapped reads with insertion percentage = 0.32% number of deletions = 50,620 mapped reads with deletion percentage = 1.05% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0901X std coverageData = 0.7387X There is a 6.92% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 27658013 0.11096467037488345 1.562570255536558 chr2 243199373 22344182 0.09187598522303757 0.8385626742449943 chr3 198022430 15085276 0.07617963278200353 0.3556557758530975 chr4 191154276 15699458 0.08212977668362491 0.469292606216324 chr5 180915260 15551428 0.0859597360664877 0.3751201336880289 chr6 171115067 12010113 0.07018734942844046 0.5201581656603302 chr7 159138663 14001383 0.08798228372699098 0.976777565515975 chr8 146364022 25374814 0.1733678376233744 0.7277238466117898 chr9 141213431 12210058 0.08646527397241698 0.5897048279459248 chr10 135534747 14803032 0.10921946089588377 0.7623456672784943 chr11 135006516 9633700 0.07135729656189335 0.674680887342006 chr12 133851895 12943452 0.09669980391387062 0.39855739116744987 chr13 115169878 6118377 0.05312480230290771 0.2885705312897097 chr14 107349540 6698686 0.06240069589492419 0.3310093169934229 chr15 102531392 7488733 0.07303844075383274 0.358630251907096 chr16 90354753 8663385 0.09588189566518986 0.4625172637640685 chr17 81195210 9571130 0.11787801275469328 0.49583448991568424 chr18 78077248 6613821 0.08470868491676346 1.2306175980625844 chr19 59128983 5717758 0.09669975213339962 1.0196383592137588 chr20 63025520 7634962 0.12114080137696603 0.4511103169825248 chr21 48129895 3746527 0.07784199404548878 0.43243141891730497 chr22 51304566 2380850 0.046406200960748795 0.26886168439933733 chrMT 16571 19709 1.1893669663870616 1.52217224369425 chrX 155270560 16046374 0.1033446005475861 0.5014021924108238 chrY 59373566 922897 0.015543903830873153 0.42254051485496824