BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716606.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 = 920,273 number of mapped reads = 715,255 (77.72%) number of supplementary alignments = 22,474 (2.44%) number of secondary alignments = 0 number of mapped bases = 53,907,042 bp number of sequenced bases = 53,885,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,648 duplication rate = 1.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6812 >>>>>>> ACTG content number of A's = 13,955,201 bp (25.9%) number of C's = 10,699,387 bp (19.86%) number of T's = 16,604,581 bp (30.81%) number of G's = 12,620,166 bp (23.42%) number of N's = 6,639 bp (0.01%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 424,962 number of insertions = 5,002 mapped reads with insertion percentage = 0.69% number of deletions = 12,050 mapped reads with deletion percentage = 1.66% homopolymer indels = 40.37% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.1707X There is a 1.63% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5530552 0.022188719040342933 0.21303037000047237 chr2 243199373 4968318 0.02042899181323136 0.23656594499484324 chr3 198022430 3975169 0.02007433703343606 0.148234402470074 chr4 191154276 2183115 0.011420696652373082 0.1195280234670291 chr5 180915260 3170546 0.017525033543328516 0.138091199834583 chr6 171115067 3025604 0.01768169251863718 0.14696775246965432 chr7 159138663 2950987 0.018543494989649374 0.2277910334104561 chr8 146364022 3954594 0.02701889402847921 0.2132848132656313 chr9 141213431 2845918 0.020153309638089596 0.17106303143520768 chr10 135534747 3262602 0.02407207061079326 0.21395200429047936 chr11 135006516 2112707 0.015648926159978826 0.1512615823686059 chr12 133851895 2303856 0.017211978956293447 0.13669903833528688 chr13 115169878 1515303 0.013157112140033698 0.1192070212170884 chr14 107349540 1338676 0.012470253715106744 0.1219915953116693 chr15 102531392 1085558 0.010587567171622911 0.10722418347577226 chr16 90354753 1476135 0.01633710403701729 0.13945364686902975 chr17 81195210 1613038 0.019866171908416764 0.15626457823013784 chr18 78077248 1272028 0.016291916436398986 0.22483942101191265 chr19 59128983 912813 0.015437657705020903 0.1961072367714545 chr20 63025520 954582 0.01514595992226641 0.1320742564214014 chr21 48129895 734040 0.015251227953021713 0.13419854643503465 chr22 51304566 766658 0.014943270351414725 0.12785639826611586 chrMT 16571 3094 0.1867117253032406 0.50093834598149 chrX 155270560 1818672 0.011712922269360012 0.12430648388388585 chrY 59373566 132477 0.0022312454670484166 0.09504906530305386