BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524417.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 = 1,778,619 number of mapped reads = 1,646,837 (92.59%) number of supplementary alignments = 6,687 (0.38%) number of secondary alignments = 0 number of mapped bases = 96,468,580 bp number of sequenced bases = 96,439,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,091 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8939 >>>>>>> ACTG content number of A's = 24,850,742 bp (25.77%) number of C's = 17,997,973 bp (18.66%) number of T's = 30,909,452 bp (32.05%) number of G's = 22,669,161 bp (23.51%) number of N's = 12,555 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 474,948 number of insertions = 7,845 mapped reads with insertion percentage = 0.47% number of deletions = 18,099 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.3187X There is a 2.76% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7931799 0.03182258470682005 0.6827323618920806 chr2 243199373 7814505 0.03213209353134311 0.342128268713245 chr3 198022430 6744985 0.034061722199853824 0.2014055863035578 chr4 191154276 6541992 0.034223623645227796 0.23178104378264158 chr5 180915260 5758719 0.03183102962127131 0.19581315724521997 chr6 171115067 3682719 0.02152188620538015 0.1779306403209182 chr7 159138663 5476581 0.03441389349865281 0.4438985963849173 chr8 146364022 5141435 0.03512772421626949 0.29908433977355653 chr9 141213431 3531234 0.025006360761817337 0.2321597810189405 chr10 135534747 4841783 0.03572355508215174 0.2853462268246519 chr11 135006516 3947591 0.029240003497312678 0.23679410364359457 chr12 133851895 4506582 0.0336684213548116 0.2083382244814788 chr13 115169878 3143549 0.027294888686085088 0.18137779472205864 chr14 107349540 2805715 0.026136255451117908 0.18289615971642914 chr15 102531392 2880038 0.028089328973510862 0.1839562940855476 chr16 90354753 2958329 0.03274126597413199 0.20792278739712383 chr17 81195210 2604323 0.032074835449036956 0.216092375739577 chr18 78077248 2754889 0.0352841457731707 0.4060888295801412 chr19 59128983 2643803 0.044712472054525276 0.47102682655378336 chr20 63025520 2598830 0.041234566569224654 0.23119340074178588 chr21 48129895 1251389 0.026000243715470394 0.19654154575302896 chr22 51304566 664042 0.012943136484187392 0.12394498019332525 chrMT 16571 138791 8.375535574195885 5.164764940416593 chrX 155270560 5805703 0.03739088079543218 0.24100663481262424 chrY 59373566 299254 0.005040189096945937 0.1473636962380871