BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716333.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 = 1,012,094 number of mapped reads = 925,585 (91.45%) number of supplementary alignments = 3,986 (0.39%) number of secondary alignments = 0 number of mapped bases = 53,770,136 bp number of sequenced bases = 53,755,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,373 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.277 >>>>>>> ACTG content number of A's = 13,719,033 bp (25.52%) number of C's = 9,942,569 bp (18.5%) number of T's = 17,260,010 bp (32.11%) number of G's = 12,833,488 bp (23.87%) number of N's = 787 bp (0%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 274,296 number of insertions = 3,389 mapped reads with insertion percentage = 0.37% number of deletions = 8,557 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.1798X There is a 1.61% of reference with a coverageData >= 1X There is a 0.09% 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 4457213 0.017882454944816367 0.3126371383807318 chr2 243199373 4484684 0.018440360041553232 0.1775279044783452 chr3 198022430 3682017 0.018593939080537494 0.14362080277165434 chr4 191154276 3573590 0.018694794983294016 0.1514444276613201 chr5 180915260 3522755 0.01947185107547036 0.14839769616898774 chr6 171115067 3317413 0.019387030365946675 0.1548234110784684 chr7 159138663 2888324 0.018149731470346712 0.19315786170692634 chr8 146364022 2656595 0.018150601245434484 0.20896634000560071 chr9 141213431 2199151 0.015573242463034554 0.16254171716428265 chr10 135534747 2493326 0.018396212448753085 0.17747332677774108 chr11 135006516 2350129 0.01740752275986442 0.16451961631455314 chr12 133851895 2364487 0.01766494975659478 0.14353662928354596 chr13 115169878 1676907 0.01456029153734104 0.12704571961183114 chr14 107349540 1812033 0.01687974629420862 0.14175113794684438 chr15 102531392 1508248 0.014710109465791706 0.12823026305618332 chr16 90354753 1491859 0.016511129193170392 0.1406537168679861 chr17 81195210 1272263 0.01566918787450639 0.13485765124207497 chr18 78077248 1453139 0.018611555058907815 0.27037668755978056 chr19 59128983 985286 0.01666333412161004 0.23008793071317424 chr20 63025520 1096529 0.017398174580709528 0.14175743277345865 chr21 48129895 753016 0.015645494344003866 0.13808981524421823 chr22 51304566 552072 0.010760679663482584 0.10919055797653535 chrMT 16571 2797 0.16878884798744795 0.4195524217991908 chrX 155270560 3029259 0.019509551585310182 0.15714758052251404 chrY 59373566 147044 0.0024765903398829034 0.07050703064049019