BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524708.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 = 612,026 number of mapped reads = 567,522 (92.73%) number of supplementary alignments = 2,318 (0.38%) number of secondary alignments = 0 number of mapped bases = 34,134,971 bp number of sequenced bases = 34,124,026 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,447 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2388 >>>>>>> ACTG content number of A's = 9,411,874 bp (27.58%) number of C's = 6,484,793 bp (19%) number of T's = 10,253,566 bp (30.05%) number of G's = 7,968,843 bp (23.35%) number of N's = 4,950 bp (0.01%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 169,818 number of insertions = 3,073 mapped reads with insertion percentage = 0.54% number of deletions = 6,775 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.011X std coverageData = 0.1358X There is a 1.04% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2753310 0.011046351615709715 0.21452426432438204 chr2 243199373 2870685 0.011803833885706605 0.15669615478525134 chr3 198022430 2302243 0.011626172853246979 0.11173098426546703 chr4 191154276 2191527 0.01146470299204816 0.11791997755393298 chr5 180915260 2120426 0.011720548062114826 0.11227724435488952 chr6 171115067 1978447 0.011562085295504692 0.11762722481175501 chr7 159138663 1871343 0.011759197700435625 0.15004944891467262 chr8 146364022 1712228 0.011698421351115918 0.1484417049740021 chr9 141213431 1407489 0.009967104333014896 0.11867020739170434 chr10 135534747 1732535 0.012782958159061603 0.14615806396366657 chr11 135006516 1572791 0.011649741409518338 0.12691614522425926 chr12 133851895 1576307 0.011776501184387415 0.11257018336995932 chr13 115169878 1046013 0.009082348771785622 0.09841142220631978 chr14 107349540 1052566 0.009805035028561837 0.10340691450282874 chr15 102531392 973497 0.009494623851395679 0.10072145045842093 chr16 90354753 978530 0.010829867466961036 0.11346390462519969 chr17 81195210 909596 0.011202582024235174 0.11246196792676401 chr18 78077248 895694 0.011471895115975399 0.19150291046476528 chr19 59128983 675971 0.011432143184333138 0.1677391047882389 chr20 63025520 685530 0.010877022514054624 0.10887780980216763 chr21 48129895 444548 0.009236421562939209 0.10545910437086432 chr22 51304566 393122 0.007662514872457941 0.0903903245495991 chrMT 16571 9309 0.5617645283929756 0.7969235139995212 chrX 155270560 1865357 0.01201359098595381 0.11685247537928511 chrY 59373566 115907 0.0019521650426049869 0.08297538927850591