BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716145.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 = 1,659,740 number of mapped reads = 1,537,486 (92.63%) number of supplementary alignments = 8,469 (0.51%) number of secondary alignments = 0 number of mapped bases = 90,948,239 bp number of sequenced bases = 90,922,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,769 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2208 >>>>>>> ACTG content number of A's = 23,227,001 bp (25.55%) number of C's = 19,142,711 bp (21.05%) number of T's = 26,932,945 bp (29.62%) number of G's = 21,619,200 bp (23.78%) number of N's = 676 bp (0%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 436,108 number of insertions = 5,746 mapped reads with insertion percentage = 0.37% number of deletions = 15,844 mapped reads with deletion percentage = 1.02% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 0.2667X There is a 2.46% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 10347825 0.04151574410721328 0.3932529438413716 chr2 243199373 10901820 0.044826678068779394 0.39303480573974375 chr3 198022430 5516290 0.0278568947972207 0.1923808467319277 chr4 191154276 3782364 0.01978697039453096 0.19135544353456557 chr5 180915260 6259013 0.03459637954255489 0.2160380187848154 chr6 171115067 3281158 0.019175155394118508 0.17425597199861959 chr7 159138663 5890948 0.03701770449083137 0.3816123487550788 chr8 146364022 3868276 0.026429145271779975 0.2451619580878481 chr9 141213431 2434872 0.017242495864292117 0.19996202455178397 chr10 135534747 4007583 0.029568675846644698 0.24641928301479304 chr11 135006516 3843465 0.028468737020070942 0.2523790057341602 chr12 133851895 3510278 0.026225090051956307 0.19018629096481507 chr13 115169878 2455042 0.021316702271751992 0.17146225317526215 chr14 107349540 1898371 0.017684016158802357 0.16099867974432092 chr15 102531392 3961466 0.03863661579860342 0.22851605651785653 chr16 90354753 2686583 0.029733720814886185 0.21033518501602538 chr17 81195210 3485955 0.042933012920343454 0.25781859431228943 chr18 78077248 2825282 0.036185727242845446 0.45696772194167484 chr19 59128983 1476951 0.024978461070436473 0.29092607124973874 chr20 63025520 2439747 0.03871046204775462 0.23130557629000056 chr21 48129895 1142029 0.02372805924467527 0.19364042214287738 chr22 51304566 1346314 0.026241601965797744 0.18989688293567084 chrMT 16571 128814 7.773459658439442 5.660452780171701 chrX 155270560 3229830 0.020801303221937243 0.18138442404624558 chrY 59373566 227963 0.003839469571357732 0.10621695952919456