BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716202.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 = 2,048,109 number of mapped reads = 1,765,957 (86.22%) number of supplementary alignments = 45,232 (2.21%) number of secondary alignments = 0 number of mapped bases = 131,700,282 bp number of sequenced bases = 131,654,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,440 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0269 >>>>>>> ACTG content number of A's = 34,184,670 bp (25.97%) number of C's = 27,356,939 bp (20.78%) number of T's = 40,144,128 bp (30.49%) number of G's = 29,952,472 bp (22.75%) number of N's = 16,293 bp (0.01%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 999,544 number of insertions = 10,651 mapped reads with insertion percentage = 0.6% number of deletions = 27,037 mapped reads with deletion percentage = 1.51% homopolymer indels = 40.18% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.3364X There is a 3.68% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% 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 10557493 0.04235693759816149 0.38497540200275954 chr2 243199373 11116757 0.04571046735387759 0.49345177503723325 chr3 198022430 8668016 0.0437728998679594 0.23377585315574284 chr4 191154276 8468609 0.04430248267111744 0.25621700866054253 chr5 180915260 7973720 0.04407433623896624 0.2361900077118794 chr6 171115067 7500827 0.043834988534352734 0.2621728418956547 chr7 159138663 7237454 0.04547891671051679 0.4244801358558124 chr8 146364022 6697751 0.04576091110696589 0.4266594427255991 chr9 141213431 5567337 0.03942498217467714 0.36484823494316176 chr10 135534747 6183096 0.04562000621139611 0.31331841348423134 chr11 135006516 6026635 0.04463958613671654 0.3626909926449509 chr12 133851895 6022051 0.04499040525350799 0.24271725607859757 chr13 115169878 4217285 0.03661795144039312 0.2129481636179289 chr14 107349540 3998239 0.03724505014180778 0.26179597732387 chr15 102531392 3717875 0.036260845849044945 0.21562353049957114 chr16 90354753 3970897 0.04394784854317514 0.26230805586892736 chr17 81195210 3574558 0.04402424724315634 0.25812552653220594 chr18 78077248 3626761 0.046450932799270796 0.6661914596601192 chr19 59128983 2705142 0.04574984825969356 0.3515188787619764 chr20 63025520 2768984 0.043934330093587486 0.2500494568240708 chr21 48129895 1698364 0.03528709131819215 0.23067424203070336 chr22 51304566 1518636 0.029600406326407674 0.1939989387717815 chrMT 16571 8709 0.5255566954317784 0.8628045602471293 chrX 155270560 7554245 0.04865213985188177 0.3127469282406611 chrY 59373566 320841 0.005403768404276072 0.13866698497448157