BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524919.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 = 792,139 number of mapped reads = 729,327 (92.07%) number of supplementary alignments = 3,101 (0.39%) number of secondary alignments = 0 number of mapped bases = 42,440,464 bp number of sequenced bases = 42,426,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,218 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1675 >>>>>>> ACTG content number of A's = 10,764,505 bp (25.37%) number of C's = 8,288,336 bp (19.54%) number of T's = 13,332,513 bp (31.42%) number of G's = 10,040,896 bp (23.67%) number of N's = 387 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 219,087 number of insertions = 3,086 mapped reads with insertion percentage = 0.42% number of deletions = 8,218 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.72% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.1551X There is a 1.27% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 4229965 0.016970730034811025 0.24880158492090146 chr2 243199373 3865934 0.01589615117963318 0.18699875886954165 chr3 198022430 2716572 0.013718506534840523 0.12449782618939037 chr4 191154276 1976848 0.010341636302187663 0.12283865205162056 chr5 180915260 2656949 0.014686151958657329 0.1283622870215769 chr6 171115067 2584831 0.015105805966227393 0.13521248633582156 chr7 159138663 2586548 0.016253422966108495 0.1795404240958192 chr8 146364022 3789881 0.02589352867059092 0.20846408928645027 chr9 141213431 1558310 0.011035140134793552 0.1305149948730142 chr10 135534747 1887990 0.013929933406670985 0.16800752448794018 chr11 135006516 2216825 0.016420133380821413 0.15153616467769274 chr12 133851895 1454963 0.010869946966384002 0.11252068708949335 chr13 115169878 1053607 0.009148286151696713 0.10134815033074396 chr14 107349540 789090 0.007350660282289053 0.09156178710295766 chr15 102531392 1126056 0.010982548642273384 0.11181307398883304 chr16 90354753 1301400 0.014403226800918819 0.13160545931769516 chr17 81195210 965210 0.011887523906890567 0.11675851574858613 chr18 78077248 1126721 0.014430849304524668 0.19408159702714362 chr19 59128983 896009 0.015153465433356092 0.18984532604433077 chr20 63025520 809695 0.012847097493205928 0.12224399894480907 chr21 48129895 387836 0.008058110245202072 0.10748169774578599 chr22 51304566 803558 0.01566250458097628 0.13333879154155132 chrMT 16571 1258 0.07591575644197694 0.2803587857075859 chrX 155270560 1540864 0.009923735703664623 0.11151611098414996 chrY 59373566 113544 0.0019123661866629336 0.08358364851630827