BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716162.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 = 4,432,314 number of mapped reads = 3,950,624 (89.13%) number of supplementary alignments = 22,725 (0.51%) number of secondary alignments = 0 number of mapped bases = 224,546,377 bp number of sequenced bases = 224,485,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,122 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8889 >>>>>>> ACTG content number of A's = 57,270,364 bp (25.51%) number of C's = 44,962,963 bp (20.03%) number of T's = 68,064,335 bp (30.32%) number of G's = 54,183,948 bp (24.14%) number of N's = 3,428 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,244,105 number of insertions = 14,725 mapped reads with insertion percentage = 0.37% number of deletions = 36,899 mapped reads with deletion percentage = 0.93% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.0725X std coverageData = 0.6233X There is a 5.96% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 16013630 0.06424710171534538 1.1150366777716632 chr2 243199373 18612611 0.07653231490855858 0.7772111624791233 chr3 198022430 13826087 0.06982081272308395 0.30829983894593893 chr4 191154276 13677960 0.07155455941775532 0.399617198998086 chr5 180915260 12236672 0.06763758900161324 0.3122759015168047 chr6 171115067 12324549 0.07202491993297118 0.38833145699999017 chr7 159138663 14259746 0.08960579240256655 0.860715047564057 chr8 146364022 9838180 0.06721720177927333 0.5464139605640521 chr9 141213431 10603939 0.07509157538987916 0.7147113354437675 chr10 135534747 9135135 0.06740068655604603 0.6801334817301521 chr11 135006516 8741194 0.0647464600893782 0.47066827364133784 chr12 133851895 16662609 0.12448541725912808 0.515353256225007 chr13 115169878 8233985 0.07149425824693502 0.30827988465788175 chr14 107349540 6103865 0.05685972198856185 0.414457029692969 chr15 102531392 5730779 0.05589292106753022 0.2810124503599415 chr16 90354753 6501049 0.07195027139302788 0.40002685379214875 chr17 81195210 7173002 0.08834267440160572 0.3796796648007602 chr18 78077248 7007646 0.08975272796500204 1.2334604728357046 chr19 59128983 4144436 0.07009144737023466 0.9128590462145474 chr20 63025520 6983575 0.11080551179902998 0.4225086550277216 chr21 48129895 2682242 0.05572923024245118 0.3698782668049341 chr22 51304566 1628471 0.0317412489172991 0.20280492490395713 chrMT 16571 32854 1.9826202401786253 1.9305576815393877 chrX 155270560 11732616 0.0755623989505802 0.47002967364433496 chrY 59373566 659545 0.01110839460105866 0.2612589794805131