BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231781.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 13,013,254 number of mapped reads = 11,778,248 (90.51%) number of supplementary alignments = 99,180 (0.76%) number of secondary alignments = 0 number of mapped bases = 788,914,682 bp number of sequenced bases = 788,595,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,130,105 duplication rate = 6.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0103 >>>>>>> ACTG content number of A's = 227,260,180 bp (28.82%) number of C's = 151,227,537 bp (19.18%) number of T's = 236,125,584 bp (29.94%) number of G's = 173,922,694 bp (22.05%) number of N's = 59,993 bp (0.01%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 4,693,295 number of insertions = 56,510 mapped reads with insertion percentage = 0.47% number of deletions = 184,061 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.2548X std coverageData = 14.9642X There is a 14.77% of reference with a coverageData >= 1X There is a 5.73% of reference with a coverageData >= 2X There is a 2.3% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 60078270 0.24103558803169442 5.6786175261860015 chr2 243199373 59265661 0.24369166856363564 52.81164686423568 chr3 198022430 61820339 0.31218856873941 0.8515645879897429 chr4 191154276 38429291 0.20103809239402 0.8558707748367349 chr5 180915260 53437293 0.29537194927614174 0.8466872582395072 chr6 171115067 62384314 0.3645752246936852 1.8652693411215333 chr7 159138663 34574271 0.21725877513499028 1.8172979244373788 chr8 146364022 51366503 0.35095033805507203 3.2346126939921054 chr9 141213431 24672402 0.17471710605204402 1.637658749088335 chr10 135534747 36679174 0.2706256130761804 2.0437352539864477 chr11 135006516 30379410 0.22502180561418236 1.342159022759084 chr12 133851895 39369868 0.29413007563322136 0.8730740572766787 chr13 115169878 32609918 0.283146240721033 0.7992201962411185 chr14 107349540 29866324 0.27821566818078586 1.0712105094794926 chr15 102531392 16777229 0.16363016899253646 0.6234649176843642 chr16 90354753 21510354 0.23806555035350493 1.0912804020107434 chr17 81195210 18853204 0.23219601254803085 1.012359033955021 chr18 78077248 20339896 0.2605098991193952 3.4567103372547527 chr19 59128983 15811651 0.2674094868163046 3.5571989476700203 chr20 63025520 22399882 0.355409713398636 1.0176394504370057 chr21 48129895 12871420 0.2674308763815088 0.9321098166690652 chr22 51304566 6051982 0.11796185937914376 0.49852829364049983 chrMT 16571 1151896 69.51276326111882 33.14829388911121 chrX 155270560 36304586 0.23381500008758904 0.980015530927899 chrY 59373566 1909544 0.03216151780406789 0.7165491902594004