BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716779.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 = 1,537,301 number of mapped reads = 1,266,323 (82.37%) number of supplementary alignments = 30,159 (1.96%) number of secondary alignments = 0 number of mapped bases = 95,743,397 bp number of sequenced bases = 95,708,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,425 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.187 >>>>>>> ACTG content number of A's = 24,337,435 bp (25.43%) number of C's = 19,125,888 bp (19.98%) number of T's = 29,129,085 bp (30.44%) number of G's = 23,104,275 bp (24.14%) number of N's = 11,681 bp (0.01%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 694,979 number of insertions = 8,168 mapped reads with insertion percentage = 0.64% number of deletions = 20,198 mapped reads with deletion percentage = 1.57% homopolymer indels = 41.06% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2687X There is a 2.76% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 7797652 0.031284383439911266 0.3089990179066416 chr2 243199373 8397626 0.03452980119319633 0.3883085868248365 chr3 198022430 6566272 0.03315923352723224 0.1977080903840863 chr4 191154276 6198937 0.032428973757301666 0.2080320850924281 chr5 180915260 5953787 0.03290925817976881 0.19976955194487625 chr6 171115067 5703461 0.03333114435796586 0.22187619616046966 chr7 159138663 5315763 0.033403340833647696 0.3266965816788653 chr8 146364022 4942787 0.033770505431997486 0.3314082333017631 chr9 141213431 4230470 0.02995798607853385 0.2844437217849907 chr10 135534747 4740469 0.03497604197394488 0.2807629692080623 chr11 135006516 4358782 0.032285715750193865 0.2859156595816196 chr12 133851895 4508995 0.033686448742470176 0.2035741910155772 chr13 115169878 3035150 0.026353679040972848 0.1759314080621168 chr14 107349540 2987031 0.02782527992201923 0.21129367796251924 chr15 102531392 2827464 0.02757656893997889 0.18129571490839602 chr16 90354753 2953004 0.03268233160905216 0.22040036459545928 chr17 81195210 2667014 0.03284693764570595 0.21334834021906465 chr18 78077248 2756471 0.03530440775781441 0.5317070116940597 chr19 59128983 1952747 0.03302520863583938 0.2870494900175895 chr20 63025520 2132021 0.03382790019027213 0.20748750774199975 chr21 48129895 1289307 0.026788070075781382 0.19182429236123724 chr22 51304566 1145031 0.022318305937915936 0.16438797378644465 chrMT 16571 7968 0.48084002172469975 0.9129853425160167 chrX 155270560 3062445 0.019723281734798922 0.19771311540003306 chrY 59373566 212743 0.003583126538163465 0.11279255924775484