BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524289.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 = 568,787 number of mapped reads = 519,418 (91.32%) number of supplementary alignments = 1,880 (0.33%) number of secondary alignments = 0 number of mapped bases = 30,307,350 bp number of sequenced bases = 30,297,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,545 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.757 >>>>>>> ACTG content number of A's = 7,881,785 bp (26.01%) number of C's = 5,560,995 bp (18.35%) number of T's = 9,825,799 bp (32.43%) number of G's = 7,027,912 bp (23.2%) number of N's = 663 bp (0%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 153,802 number of insertions = 2,390 mapped reads with insertion percentage = 0.46% number of deletions = 6,344 mapped reads with deletion percentage = 1.21% homopolymer indels = 43.67% >>>>>>> Coverage mean coverageData = 0.0098X std coverageData = 0.1262X There is a 0.93% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2440436 0.009791092957798488 0.19016720212133828 chr2 243199373 2534753 0.010422530982429795 0.1537306103669722 chr3 198022430 2040182 0.010302782366623821 0.1049702942984903 chr4 191154276 1995256 0.010437935482018722 0.11001074708564042 chr5 180915260 1855084 0.010253883503248979 0.10464746158933542 chr6 171115067 1738716 0.010161092360148508 0.10931402651161765 chr7 159138663 1690783 0.01062458970137257 0.16044413855496698 chr8 146364022 1525367 0.010421734652796026 0.1393196987578738 chr9 141213431 1285069 0.009100189627146727 0.11244285884437351 chr10 135534747 1452995 0.010720461226079538 0.12766785909449932 chr11 135006516 1351321 0.01000930206953863 0.1118138295032057 chr12 133851895 1373323 0.010260019105444865 0.10506412881506651 chr13 115169878 967498 0.00840061669597323 0.09538330297867852 chr14 107349540 929806 0.008661480990044297 0.09818575712338733 chr15 102531392 861499 0.008402294977132466 0.09592842298319836 chr16 90354753 864584 0.00956877166163024 0.1053799844817061 chr17 81195210 796501 0.009809704291669422 0.10417606537760796 chr18 78077248 812105 0.010401301541775652 0.15748800478505914 chr19 59128983 616684 0.010429470772396001 0.15279101905606884 chr20 63025520 637268 0.01011126921285219 0.10466786514309599 chr21 48129895 399804 0.00830677066717058 0.0977667572403687 chr22 51304566 343296 0.006691334256681949 0.08460604110961498 chrMT 16571 2643 0.159495504194074 0.39889809403241483 chrX 155270560 1692161 0.010898144503375269 0.11147431892217498 chrY 59373566 100216 0.0016878891862415674 0.06254350538285891