BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524353.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 = 3,136,432 number of mapped reads = 2,891,763 (92.2%) number of supplementary alignments = 18,803 (0.6%) number of secondary alignments = 0 number of mapped bases = 171,036,360 bp number of sequenced bases = 170,986,624 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 196,323 duplication rate = 4.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2501 >>>>>>> ACTG content number of A's = 43,789,446 bp (25.61%) number of C's = 33,070,776 bp (19.34%) number of T's = 54,050,916 bp (31.61%) number of G's = 40,050,416 bp (23.42%) number of N's = 25,070 bp (0.01%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 893,289 number of insertions = 12,187 mapped reads with insertion percentage = 0.42% number of deletions = 31,144 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.0552X std coverageData = 0.5116X There is a 4.53% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 13868586 0.05564112917496001 1.031926658605071 chr2 243199373 14328973 0.058918626406162654 0.6328355146855119 chr3 198022430 11230572 0.05671363592498082 0.28325000680748247 chr4 191154276 10932641 0.05719276193434459 0.36120393667734874 chr5 180915260 10160803 0.05616332751587677 0.2820967563902598 chr6 171115067 9670887 0.05651686417537972 0.3119252344725767 chr7 159138663 9472647 0.05952448525975111 0.7026563422536329 chr8 146364022 8732756 0.05966463534324029 0.4592232629517263 chr9 141213431 7240451 0.051273104468370294 0.41117644327410535 chr10 135534747 8301210 0.06124783632052672 0.5042497894443252 chr11 135006516 7850468 0.05814880816567402 0.43247441184772595 chr12 133851895 7620646 0.056933418835796085 0.2924700936882115 chr13 115169878 5286743 0.045903869065486026 0.2526359597529374 chr14 107349540 5154117 0.04801247401712201 0.2961560879628236 chr15 102531392 4986851 0.0486373090497006 0.2617791310529797 chr16 90354753 5159364 0.05710119090248634 0.32596034040229016 chr17 81195210 4788415 0.05897410697010329 0.32728235787224985 chr18 78077248 4554391 0.05833185872534852 0.9029758616445461 chr19 59128983 3623079 0.061274163974712706 0.6769008370474225 chr20 63025520 3728132 0.05915273685960862 0.3045333636725202 chr21 48129895 2248551 0.04671838573510289 0.3321748517200983 chr22 51304566 2187140 0.04263051362718866 0.24624243910147064 chrMT 16571 31761 1.9166616378009775 1.7074922317526715 chrX 155270560 9290785 0.05983610157649975 0.34540940199968867 chrY 59373566 586391 0.00987629747554661 0.29820498617400015