BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525164.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 = 2,379,499 number of mapped reads = 2,171,421 (91.26%) number of supplementary alignments = 7,238 (0.3%) number of secondary alignments = 0 number of mapped bases = 126,269,824 bp number of sequenced bases = 126,229,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,756 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.847 >>>>>>> ACTG content number of A's = 32,228,501 bp (25.53%) number of C's = 23,204,153 bp (18.38%) number of T's = 40,704,270 bp (32.25%) number of G's = 30,089,389 bp (23.84%) number of N's = 3,168 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 642,211 number of insertions = 9,908 mapped reads with insertion percentage = 0.45% number of deletions = 25,349 mapped reads with deletion percentage = 1.16% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.3647X There is a 3.6% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% 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 13735133 0.05510571225417328 0.6684302510124125 chr2 243199373 10648250 0.04378403557808515 0.5314871057649757 chr3 198022430 10182227 0.051419563935257234 0.2566215225983125 chr4 191154276 7245666 0.03790480731908922 0.23157184518226387 chr5 180915260 5795911 0.032036606530593384 0.1986687393796787 chr6 171115067 6468594 0.03780259747670262 0.25359531951266867 chr7 159138663 7578105 0.04761950903156702 0.5410010279684002 chr8 146364022 5932883 0.04053511866461281 0.3234487179582811 chr9 141213431 4259253 0.03016181229956802 0.26322085580215565 chr10 135534747 6931580 0.05114245721800034 0.3910103562933088 chr11 135006516 5831030 0.04319073014223995 0.29652155605463154 chr12 133851895 5888884 0.043995522065638296 0.23796707251741406 chr13 115169878 4006755 0.03478995610293171 0.21351795792710732 chr14 107349540 4878092 0.04544120077272804 0.24786644911375197 chr15 102531392 3582056 0.03493618812860748 0.2157463482903055 chr16 90354753 3514978 0.03890197121118797 0.24467826721963248 chr17 81195210 2589764 0.03189552684203908 0.2108577240857302 chr18 78077248 2790363 0.03573849068040923 0.5229649212516705 chr19 59128983 2332926 0.039454864292186455 0.4578531587950703 chr20 63025520 2350650 0.037296796599218855 0.21955515613796708 chr21 48129895 1657163 0.034431053714120925 0.22015481406062515 chr22 51304566 1065541 0.02076893117076558 0.15971907873065172 chrMT 16571 50154 3.02661275722648 2.304717135150748 chrX 155270560 6579409 0.04237383442167015 0.2553654337273762 chrY 59373566 374457 0.006306796529620606 0.16797921150661876