BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525039.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 = 1,106,667 number of mapped reads = 1,013,084 (91.54%) number of supplementary alignments = 4,274 (0.39%) number of secondary alignments = 0 number of mapped bases = 59,003,445 bp number of sequenced bases = 58,984,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,875 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.434 >>>>>>> ACTG content number of A's = 15,557,882 bp (26.38%) number of C's = 10,546,290 bp (17.88%) number of T's = 18,397,939 bp (31.19%) number of G's = 14,481,462 bp (24.55%) number of N's = 534 bp (0%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 291,419 number of insertions = 4,085 mapped reads with insertion percentage = 0.4% number of deletions = 11,410 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.17% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.1905X There is a 1.76% of reference with a coverageData >= 1X There is a 0.1% 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 4898881 0.01965443849385635 0.314576870385972 chr2 243199373 4961140 0.020399476934506736 0.2128623563842753 chr3 198022430 3848512 0.019434727672011702 0.14848683713607155 chr4 191154276 3829174 0.020031851131595925 0.1621796941228027 chr5 180915260 3358658 0.01856481316169791 0.14545678748732094 chr6 171115067 3445058 0.020132990392950027 0.17714932569946187 chr7 159138663 3432275 0.02156782604111736 0.23243417626740984 chr8 146364022 2726924 0.018631108675054037 0.19138631537112205 chr9 141213431 2347255 0.01662203788533401 0.16050330352858105 chr10 135534747 2859731 0.021099615141495782 0.19943703551035225 chr11 135006516 2751684 0.020381860679968958 0.18486373638330292 chr12 133851895 2706683 0.02022147687935236 0.15281928747847434 chr13 115169878 1745340 0.015154483362394462 0.13113644999626972 chr14 107349540 1704877 0.015881549189684464 0.13679634964363813 chr15 102531392 1638547 0.015980930016048157 0.13558971151347207 chr16 90354753 1812875 0.020063969407342633 0.15868269341125124 chr17 81195210 1697737 0.02090932457715178 0.16587129904396272 chr18 78077248 1643120 0.021044799119968982 0.26300809136386777 chr19 59128983 1284190 0.02171845235356069 0.2314256958099001 chr20 63025520 1334290 0.021170630563619307 0.15767667077407535 chr21 48129895 787013 0.016351853666001143 0.14714621170312484 chr22 51304566 751979 0.014657155466435482 0.12815780963090453 chrMT 16571 9765 0.5892824814434856 0.851712383548495 chrX 155270560 3242330 0.020881807858489077 0.16605553886675237 chrY 59373566 185407 0.0031227196291359694 0.10086440628135317