BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716952.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 = 1,866,605 number of mapped reads = 1,706,615 (91.43%) number of supplementary alignments = 5,646 (0.3%) number of secondary alignments = 0 number of mapped bases = 98,119,770 bp number of sequenced bases = 98,088,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,881 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0119 >>>>>>> ACTG content number of A's = 24,701,600 bp (25.18%) number of C's = 17,877,006 bp (18.23%) number of T's = 32,107,526 bp (32.73%) number of G's = 23,400,856 bp (23.86%) number of N's = 1,918 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 503,619 number of insertions = 7,445 mapped reads with insertion percentage = 0.43% number of deletions = 19,218 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.3032X There is a 2.84% of reference with a coverageData >= 1X There is a 0.23% 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 0.01% 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 8779614 0.035224040625359165 0.4898902991488919 chr2 243199373 7814623 0.03213257872996243 0.45063611323019526 chr3 198022430 5462842 0.027586985979315574 0.1865976629907292 chr4 191154276 6058488 0.03169423214995201 0.23835049581278656 chr5 180915260 5405929 0.029881000640852518 0.1898374495527337 chr6 171115067 5453889 0.03187264041453462 0.23842033799141008 chr7 159138663 5591152 0.03513383796620184 0.37790933571730917 chr8 146364022 5393615 0.036850688620732215 0.3843164787564626 chr9 141213431 3308722 0.023430646621708386 0.2217826627953269 chr10 135534747 4447444 0.032814050259746305 0.322699663919297 chr11 135006516 3776200 0.02797050180896454 0.24565631188372816 chr12 133851895 4677692 0.03494677456751733 0.2061610125031154 chr13 115169878 2839793 0.024657428220945063 0.17212653828179295 chr14 107349540 3418136 0.031841179757267704 0.20100193009667103 chr15 102531392 3509821 0.034231672188747814 0.20732396685095014 chr16 90354753 3164125 0.03501891040529988 0.2166310841805524 chr17 81195210 4053689 0.049925223421430895 0.25795781002539625 chr18 78077248 1795391 0.022995059969326787 0.37778836605520394 chr19 59128983 2329670 0.03939979823431091 0.40148287303180735 chr20 63025520 3092190 0.04906250674330018 0.2541657407929686 chr21 48129895 1257065 0.026118174577359873 0.21616977205146354 chr22 51304566 864609 0.01685247663921375 0.14150197188954144 chrMT 16571 88140 5.31893066199988 3.778465805441956 chrX 155270560 5175273 0.033330677753722275 0.22123440352774118 chrY 59373566 361658 0.006091229218066504 0.2541678496560961