BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716934.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 = 1,312,369 number of mapped reads = 941,925 (71.77%) number of supplementary alignments = 1,092 (0.08%) number of secondary alignments = 0 number of mapped bases = 49,921,426 bp number of sequenced bases = 49,907,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,359 duplication rate = 6.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6596 >>>>>>> ACTG content number of A's = 11,015,257 bp (22.07%) number of C's = 8,892,720 bp (17.82%) number of T's = 16,492,762 bp (33.05%) number of G's = 13,506,027 bp (27.06%) number of N's = 915 bp (0%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 354,126 number of insertions = 3,028 mapped reads with insertion percentage = 0.32% number of deletions = 8,003 mapped reads with deletion percentage = 0.85% homopolymer indels = 39.01% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.1695X There is a 1.39% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.03% 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 4721845 0.01894416543901008 0.19277952828156417 chr2 243199373 4141977 0.017031199336192366 0.257089390979338 chr3 198022430 3182339 0.016070598669049765 0.14655892125638664 chr4 191154276 3133566 0.01639286374111767 0.1577844349455712 chr5 180915260 4216671 0.02330743686298215 0.1745775505849634 chr6 171115067 2084612 0.012182515757072403 0.150355984712106 chr7 159138663 2702368 0.01698121593493594 0.17074565201503347 chr8 146364022 2870517 0.019612176276489587 0.1656485262809954 chr9 141213431 2154766 0.015258931000692137 0.1516069670390471 chr10 135534747 2472239 0.018240628729693942 0.19203394001162716 chr11 135006516 2081523 0.015417944716090592 0.15848602393111202 chr12 133851895 2261486 0.01689543506276097 0.15093784264775426 chr13 115169878 797927 0.006928261224692797 0.0972189106306699 chr14 107349540 2172825 0.020240654966942568 0.16645172961756471 chr15 102531392 950689 0.009272174906198484 0.11186586328805043 chr16 90354753 1293769 0.014318770812200659 0.15849354040922062 chr17 81195210 1911789 0.023545588465132366 0.1833841278419663 chr18 78077248 1263438 0.016181897189818984 0.16740175243451974 chr19 59128983 1291786 0.02184691727236371 0.21182413019121993 chr20 63025520 1244637 0.01974814329179672 0.1696607366604272 chr21 48129895 689253 0.014320683641632711 0.15119518392339182 chr22 51304566 532378 0.010376815194187589 0.12198273911827642 chrMT 16571 51052 3.0808038138917384 2.8955641293525796 chrX 155270560 1531975 0.009866487246519881 0.11678768521884071 chrY 59373566 165999 0.002795840155533188 0.09172051862587763