BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716258.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 = 2,834,381 number of mapped reads = 2,606,959 (91.98%) number of supplementary alignments = 17,415 (0.61%) number of secondary alignments = 0 number of mapped bases = 152,083,724 bp number of sequenced bases = 152,040,521 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,646 duplication rate = 5.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8128 >>>>>>> ACTG content number of A's = 38,806,826 bp (25.52%) number of C's = 30,933,824 bp (20.35%) number of T's = 46,161,357 bp (30.36%) number of G's = 36,136,537 bp (23.77%) number of N's = 1,977 bp (0%) GC percentage = 44.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 750,545 number of insertions = 9,227 mapped reads with insertion percentage = 0.35% number of deletions = 27,176 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.35% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.3897X There is a 3.9% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.16% 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% 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 12279120 0.04926415007808546 0.6061884554990892 chr2 243199373 12888349 0.05299499271324191 0.5398712031461129 chr3 198022430 9946258 0.0502279362999434 0.2727954596068237 chr4 191154276 9581555 0.05012472229499067 0.33874369776941854 chr5 180915260 8983421 0.049655407730669045 0.27184581139729086 chr6 171115067 8638572 0.05048399390802915 0.30108376769541106 chr7 159138663 8279672 0.05202803544981398 0.51947344530751 chr8 146364022 7722468 0.05276206471013758 0.41533972275051 chr9 141213431 6362378 0.04505504862352647 0.32070912971692556 chr10 135534747 7319992 0.05400823155703386 0.43249902632745785 chr11 135006516 6923822 0.051285095009784565 0.3431548868635289 chr12 133851895 6806180 0.05084858903192965 0.2812536014917963 chr13 115169878 4604314 0.03997845686699434 0.2460548509969622 chr14 107349540 4629806 0.043128326399908185 0.27028789387349195 chr15 102531392 4510343 0.04398987385248802 0.2638216024851385 chr16 90354753 4549307 0.05034939335178084 0.29168889830232414 chr17 81195210 4414113 0.05436420448940276 0.3154072263350912 chr18 78077248 3919036 0.05019434086611249 0.555803540413783 chr19 59128983 3304743 0.05589040826222227 0.47622365179431747 chr20 63025520 3352457 0.05319205617026246 0.2939583167918149 chr21 48129895 1994202 0.04143374923215602 0.300373435369013 chr22 51304566 1987671 0.03874257507606633 0.24157958563012413 chrMT 16571 98621 5.951421157443727 4.501165938340506 chrX 155270560 8491781 0.05469021944662272 0.3124903212974891 chrY 59373566 495543 0.008346188942062197 0.2329523868367041