BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524500.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 = 4,311,791 number of mapped reads = 3,857,121 (89.46%) number of supplementary alignments = 14,348 (0.33%) number of secondary alignments = 0 number of mapped bases = 224,057,564 bp number of sequenced bases = 223,998,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 236,968 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7551 >>>>>>> ACTG content number of A's = 58,349,648 bp (26.05%) number of C's = 38,756,253 bp (17.3%) number of T's = 71,090,955 bp (31.74%) number of G's = 55,795,311 bp (24.91%) number of N's = 6,756 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,072,339 number of insertions = 15,285 mapped reads with insertion percentage = 0.39% number of deletions = 35,481 mapped reads with deletion percentage = 0.91% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0724X std coverageData = 0.5541X There is a 5.76% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 16432892 0.06592919180730948 0.9677450077760935 chr2 243199373 19081594 0.07846070392623915 0.6346406551014444 chr3 198022430 13419603 0.06776809576571705 0.3097040046035276 chr4 191154276 13572454 0.07100261780175925 0.40109469099380196 chr5 180915260 12218297 0.06753602211333638 0.3149222161797525 chr6 171115067 12029716 0.07030190976695232 0.3690631357464324 chr7 159138663 14444250 0.09076518381959763 0.7817583708986705 chr8 146364022 10041655 0.06860739997975732 0.5819483318070955 chr9 141213431 10208606 0.07229203290160126 0.5729345490145835 chr10 135534747 8173017 0.06030200506442824 0.5461638809794872 chr11 135006516 8616362 0.06382182323703546 0.46621054101202825 chr12 133851895 16298545 0.12176551553491267 0.5128737637798447 chr13 115169878 8211654 0.07130036206168422 0.3186292290424357 chr14 107349540 7863901 0.0732550973203984 0.3718237421429364 chr15 102531392 5813930 0.05670390196204495 0.28494470903727315 chr16 90354753 6349127 0.07026887672417188 0.3540805426613488 chr17 81195210 6726927 0.08284881583531836 0.37574012342197405 chr18 78077248 6889950 0.08824529778508587 1.0505800707135748 chr19 59128983 3702375 0.0626152321950134 0.7340645244636673 chr20 63025520 6949115 0.11025874915431083 0.4223087456142288 chr21 48129895 2749598 0.057128693091892266 0.351372191761514 chr22 51304566 2312722 0.045078287963687284 0.2506692426347583 chrMT 16571 231847 13.991129080924507 8.871858848870508 chrX 155270560 11115109 0.07158542482232305 0.39812999438977525 chrY 59373566 604318 0.010178233188823457 0.25911673694058346