BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617599.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 55,890,948 number of mapped reads = 55,285,885 (98.92%) number of supplementary alignments = 816,951 (1.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,797,112 number of mapped paired reads (second in pair) = 27,488,773 number of mapped paired reads (both in pair) = 54,878,416 number of mapped paired reads (singletons) = 407,469 number of mapped bases = 7,484,580,113 bp number of sequenced bases = 7,480,370,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,911,313 duplication rate = 20.59% >>>>>>> Insert size mean insert size = 89,515.1867 std insert size = 2,906,490.3849 median insert size = 281 >>>>>>> Mapping quality mean mapping quality = 53.624 >>>>>>> ACTG content number of A's = 2,197,760,608 bp (29.38%) number of C's = 1,398,083,995 bp (18.69%) number of T's = 2,261,273,385 bp (30.23%) number of G's = 1,622,955,647 bp (21.7%) number of N's = 296,510 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 73,946,264 number of insertions = 1,017,875 mapped reads with insertion percentage = 1.76% number of deletions = 2,143,381 mapped reads with deletion percentage = 3.75% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 2.4177X std coverageData = 31.8923X There is a 53.86% of reference with a coverageData >= 1X There is a 39.24% of reference with a coverageData >= 2X There is a 28.85% of reference with a coverageData >= 3X There is a 21.85% of reference with a coverageData >= 4X There is a 16.69% of reference with a coverageData >= 5X There is a 12.95% of reference with a coverageData >= 6X There is a 10.13% of reference with a coverageData >= 7X There is a 8.02% of reference with a coverageData >= 8X There is a 6.39% of reference with a coverageData >= 9X There is a 5.14% of reference with a coverageData >= 10X There is a 4.17% of reference with a coverageData >= 11X There is a 3.4% of reference with a coverageData >= 12X There is a 2.79% of reference with a coverageData >= 13X There is a 2.31% of reference with a coverageData >= 14X There is a 1.92% of reference with a coverageData >= 15X There is a 1.6% of reference with a coverageData >= 16X There is a 1.34% of reference with a coverageData >= 17X There is a 1.13% of reference with a coverageData >= 18X There is a 0.96% of reference with a coverageData >= 19X There is a 0.82% of reference with a coverageData >= 20X There is a 0.7% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.52% of reference with a coverageData >= 23X There is a 0.45% of reference with a coverageData >= 24X There is a 0.39% of reference with a coverageData >= 25X There is a 0.34% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 637115694 2.5561248009889614 33.26934893322561 chr2 243199373 883267011 3.6318638494187234 34.45613118024136 chr3 198022430 534952767 2.7014756207162995 4.79138382627856 chr4 191154276 436925326 2.2857209116263766 19.818203570884524 chr5 180915260 394906741 2.1828271479144434 4.261273427580662 chr6 171115067 520378661 3.041103686094457 12.586841409975763 chr7 159138663 462703122 2.907546873131641 45.65158973747585 chr8 146364022 473673302 3.2362686917690744 9.101699114860649 chr9 141213431 288526910 2.0431973641374097 47.26168697883226 chr10 135534747 355899466 2.6258909532623393 99.22520596112187 chr11 135006516 338052583 2.5039723490086954 37.26836542665331 chr12 133851895 385107170 2.877114067006672 7.8387410410114375 chr13 115169878 229690412 1.9943618590965253 3.3921772174757496 chr14 107349540 171532058 1.5978834934923802 3.4249596943115925 chr15 102531392 212296142 2.0705477401496704 4.6632765110988865 chr16 90354753 163864325 1.8135661883774947 15.724448316170461 chr17 81195210 179301301 2.2082743674165015 34.44403748451047 chr18 78077248 171979639 2.2026857170990453 37.11417034078027 chr19 59128983 67419944 1.1402182242843582 17.72302365695845 chr20 63025520 171070155 2.7142997788832206 6.609178687287504 chr21 48129895 76153294 1.5822451721533985 7.631140640575853 chr22 51304566 65754792 1.281655749704617 3.036859404404581 chrMT 16571 2663617 160.739665681009 99.5899499327813 chrX 155270560 221608416 1.4272403989526412 8.289509849822984 chrY 59373566 39737265 0.6692753640567926 16.65706160662057