BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525246.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 = 1,395,187 number of mapped reads = 1,277,312 (91.55%) number of supplementary alignments = 3,765 (0.27%) number of secondary alignments = 0 number of mapped bases = 74,050,775 bp number of sequenced bases = 74,027,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,102 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2913 >>>>>>> ACTG content number of A's = 19,758,906 bp (26.69%) number of C's = 12,706,729 bp (17.16%) number of T's = 23,721,153 bp (32.04%) number of G's = 17,838,929 bp (24.1%) number of N's = 1,581 bp (0%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 363,753 number of insertions = 6,511 mapped reads with insertion percentage = 0.51% number of deletions = 14,843 mapped reads with deletion percentage = 1.15% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2306X There is a 2.18% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7485270 0.030031098698847375 0.33469041105649044 chr2 243199373 6103129 0.025095167494531327 0.31019178548972026 chr3 198022430 5556518 0.028060043501132673 0.1807804675107104 chr4 191154276 4339264 0.022700324004261353 0.16622072265626903 chr5 180915260 3533774 0.019532758043738267 0.14957512439599632 chr6 171115067 4864377 0.028427520061690418 0.2009865417190269 chr7 159138663 5662234 0.03558050503415377 0.4297565852114344 chr8 146364022 3852714 0.026322821328317966 0.2514358869670689 chr9 141213431 2325103 0.016465168954077746 0.16354758575587255 chr10 135534747 3550102 0.026193297870692894 0.23649264189274177 chr11 135006516 3632355 0.026905034716990992 0.19951947278471405 chr12 133851895 3465159 0.025888008533610972 0.17395447032681985 chr13 115169878 1851692 0.01607791926288226 0.13819850315695842 chr14 107349540 3574365 0.03329650970092653 0.1980274911119712 chr15 102531392 1505754 0.014685785208104851 0.13768093092133452 chr16 90354753 1862211 0.02060999491637147 0.16540799225805997 chr17 81195210 1132515 0.013948051861680019 0.13119219738573348 chr18 78077248 1700832 0.021783964516782148 0.27032106847549525 chr19 59128983 1050001 0.01775780584624633 0.2590134597174114 chr20 63025520 1328944 0.021085807780721208 0.15835621115195384 chr21 48129895 883120 0.018348679131753767 0.14932910586933132 chr22 51304566 511589 0.009971607595316175 0.10668067865884737 chrMT 16571 4598 0.27747269325930846 0.553397316999685 chrX 155270560 4078937 0.02626986725622681 0.1862415446995284 chrY 59373566 196218 0.0033048040267616738 0.09411867747859949