BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524368.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 = 2,515,320 number of mapped reads = 2,319,912 (92.23%) number of supplementary alignments = 11,541 (0.46%) number of secondary alignments = 0 number of mapped bases = 136,613,775 bp number of sequenced bases = 136,575,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,236 duplication rate = 6.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3353 >>>>>>> ACTG content number of A's = 33,411,201 bp (24.46%) number of C's = 27,474,926 bp (20.12%) number of T's = 42,016,961 bp (30.76%) number of G's = 33,652,636 bp (24.64%) number of N's = 19,513 bp (0.01%) GC percentage = 44.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 696,063 number of insertions = 8,535 mapped reads with insertion percentage = 0.37% number of deletions = 24,389 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.419X There is a 3.5% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 10967259 0.044000929490161635 0.7967571963641529 chr2 243199373 11562123 0.04754174674619741 0.5585838008991663 chr3 198022430 8874572 0.04481599382453796 0.25769071635927193 chr4 191154276 8529538 0.04462122521392093 0.3283365202339791 chr5 180915260 7910162 0.04372302259079748 0.2567583058578375 chr6 171115067 7763242 0.04536854723611218 0.2764825072536678 chr7 159138663 7357142 0.046231015526377775 0.5068805960865147 chr8 146364022 6925659 0.047318042407990125 0.4012050327715973 chr9 141213431 5815868 0.04118494932681014 0.34051798392797517 chr10 135534747 6632777 0.04893783436951411 0.43155493209853146 chr11 135006516 6202789 0.04594436760370885 0.3508618234110261 chr12 133851895 6122591 0.04574153395437547 0.2683991951167296 chr13 115169878 4106074 0.03565232568884027 0.2318605044779563 chr14 107349540 4116389 0.038345660354017354 0.2529781242443298 chr15 102531392 4052069 0.03952027687286251 0.24145383679899166 chr16 90354753 4284320 0.04741665333311243 0.29785729427252633 chr17 81195210 3871433 0.04768055898863985 0.29160247467078176 chr18 78077248 3593329 0.046022741477773396 0.6942234834093236 chr19 59128983 2969372 0.05021855356450152 0.5244408998949457 chr20 63025520 3401556 0.05397108980616106 0.2981142436125849 chr21 48129895 1882976 0.03912279467885812 0.2987101129142396 chr22 51304566 1865830 0.03636771822609317 0.23981136186909158 chrMT 16571 28547 1.7227083459054975 2.005306175468471 chrX 155270560 7283397 0.046907778267818445 0.29754193643604526 chrY 59373566 494761 0.00833301809764972 0.2482576916170305