BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238292.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 = 3,216,616 number of mapped reads = 181,304 (5.64%) number of supplementary alignments = 1,570 (0.05%) number of secondary alignments = 0 number of mapped bases = 11,565,433 bp number of sequenced bases = 11,556,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,373 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.058 >>>>>>> ACTG content number of A's = 3,181,914 bp (27.53%) number of C's = 2,318,406 bp (20.06%) number of T's = 3,389,207 bp (29.33%) number of G's = 2,664,529 bp (23.06%) number of N's = 2,916 bp (0.03%) GC percentage = 43.12% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 109,615 number of insertions = 2,187 mapped reads with insertion percentage = 1.08% number of deletions = 4,547 mapped reads with deletion percentage = 2.28% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.0037X std coverageData = 0.1952X There is a 0.35% of reference with a coverageData >= 1X There is a 0.01% 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 1126457 0.004519374898568457 0.1945819405384281 chr2 243199373 941125 0.003869767378059811 0.42869148058099976 chr3 198022430 720213 0.0036370273811911105 0.06131737427688908 chr4 191154276 663081 0.0034688264049086716 0.06099362291833277 chr5 180915260 731054 0.00404086421454995 0.4334567087022014 chr6 171115067 731858 0.004276993328705531 0.3226812130426445 chr7 159138663 597795 0.0037564410101899623 0.07590032166254233 chr8 146364022 507611 0.003468140551644584 0.07280883739688104 chr9 141213431 438024 0.0031018579245482678 0.06342883986430668 chr10 135534747 514547 0.003796421297042005 0.0712529304316424 chr11 135006516 452731 0.0033534011054696055 0.1368713747435169 chr12 133851895 629570 0.0047034821583960395 0.06989188518026432 chr13 115169878 286687 0.002489253309793382 0.050681067318589165 chr14 107349540 333470 0.003106394307791165 0.05920011223170148 chr15 102531392 348668 0.0034005975457740787 0.05941917223861537 chr16 90354753 370885 0.004104764693452264 0.06717054818699622 chr17 81195210 314279 0.0038706593652507336 0.07438524773718745 chr18 78077248 317374 0.004064871753676564 0.09706722126097247 chr19 59128983 258825 0.004377294972247366 0.08040300259223683 chr20 63025520 264788 0.004201282274227964 0.06685491126717973 chr21 48129895 129966 0.002700317546921721 0.056296975372484834 chr22 51304566 145670 0.002839318434152625 0.05433942398331193 chrMT 16571 972 0.05865668939713958 0.24181560568461008 chrX 155270560 706503 0.004550141379022527 0.07081363295616147 chrY 59373566 33280 5.605188005719582E-4 0.027206012309955317