BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867848.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 = 1,561,264 number of mapped reads = 1,441,302 (92.32%) number of supplementary alignments = 6,195 (0.4%) number of secondary alignments = 0 number of mapped bases = 85,065,551 bp number of sequenced bases = 85,040,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,308 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9046 >>>>>>> ACTG content number of A's = 21,316,487 bp (25.07%) number of C's = 16,681,931 bp (19.62%) number of T's = 26,513,758 bp (31.18%) number of G's = 20,516,397 bp (24.13%) number of N's = 11,640 bp (0.01%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 425,839 number of insertions = 5,797 mapped reads with insertion percentage = 0.4% number of deletions = 15,978 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2666X There is a 2.48% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6742223 0.027049974732058942 0.4677577868093683 chr2 243199373 7203054 0.029617897082325127 0.35288820709491797 chr3 198022430 5557631 0.02806566407653921 0.1800328542512069 chr4 191154276 5420200 0.02835510726424974 0.2065849065375815 chr5 180915260 5101013 0.02819559278747409 0.18227931328208719 chr6 171115067 4840050 0.028285352569215896 0.20552368350899983 chr7 159138663 4600630 0.028909568003596963 0.2999285550163207 chr8 146364022 4331484 0.02959391208858691 0.2926601034402889 chr9 141213431 3615738 0.025604774095461216 0.22624015982180792 chr10 135534747 4117702 0.030381153845367787 0.2806742237427791 chr11 135006516 3872517 0.028683926633585596 0.23244412614035248 chr12 133851895 3897029 0.029114485080693104 0.18775523075472186 chr13 115169878 2681853 0.023286062697748106 0.16734645755873498 chr14 107349540 2558290 0.023831401606378564 0.17030999790807883 chr15 102531392 2479061 0.02417855596849792 0.1688461915686569 chr16 90354753 2531370 0.028015903048287896 0.19338583309534083 chr17 81195210 2338936 0.028806329831525777 0.1950569929621289 chr18 78077248 2307494 0.02955398735365263 0.4080712474839805 chr19 59128983 1823292 0.03083584238206837 0.3644690848895563 chr20 63025520 1851677 0.029379797263076924 0.1883231469654192 chr21 48129895 1167778 0.024263048984420183 0.19601932053693574 chr22 51304566 1057341 0.020609101341974124 0.15496565374065305 chrMT 16571 21420 1.2926196367147427 1.3163458651117053 chrX 155270560 4652644 0.02996475313800633 0.20242126031783572 chrY 59373566 295124 0.004970629522235535 0.19846895934971515