BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524924.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 = 1,407,350 number of mapped reads = 1,290,565 (91.7%) number of supplementary alignments = 4,853 (0.34%) number of secondary alignments = 0 number of mapped bases = 74,814,614 bp number of sequenced bases = 74,791,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,542 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6658 >>>>>>> ACTG content number of A's = 18,912,932 bp (25.29%) number of C's = 13,913,928 bp (18.6%) number of T's = 24,184,723 bp (32.34%) number of G's = 17,778,877 bp (23.77%) number of N's = 580 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 385,011 number of insertions = 5,143 mapped reads with insertion percentage = 0.4% number of deletions = 14,223 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.73% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2392X There is a 2.15% of reference with a coverageData >= 1X There is a 0.2% 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% 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 7669182 0.03076895844524295 0.429377053643936 chr2 243199373 6701862 0.027557069400832707 0.308452438872055 chr3 198022430 4673223 0.02359946294972746 0.16872033072319154 chr4 191154276 3397525 0.01777373266816171 0.1761030208346087 chr5 180915260 4516693 0.02496579337751829 0.17292600687000204 chr6 171115067 4688802 0.027401456120751774 0.19312058421437905 chr7 159138663 4548745 0.02858353158339655 0.2839311313180895 chr8 146364022 6594933 0.045058429728037946 0.29999647795940626 chr9 141213431 2716167 0.01923448060687655 0.18774802750228298 chr10 135534747 3217318 0.023737957027359192 0.26004940202651183 chr11 135006516 3799169 0.02814063433797521 0.21373645031177282 chr12 133851895 2423487 0.01810573544737637 0.1520796095305039 chr13 115169878 2170469 0.01884580445591859 0.1524248142941076 chr14 107349540 1366688 0.012731195680950286 0.12953191734045091 chr15 102531392 1933176 0.018854479221349106 0.15104452066873844 chr16 90354753 2207634 0.02443295927110774 0.18096571729143368 chr17 81195210 1692354 0.020843027562832833 0.16322292029138388 chr18 78077248 1972509 0.02526355693274435 0.31274395869984584 chr19 59128983 1564950 0.02646671599273067 0.30186693490762895 chr20 63025520 1397557 0.02217446202744539 0.16771555141938338 chr21 48129895 654635 0.013601421735908628 0.148602195932017 chr22 51304566 1398183 0.02725260359867385 0.1819069201326306 chrMT 16571 4047 0.2442218333232756 0.4987846093950276 chrX 155270560 3295216 0.02122241331518351 0.17411100882083205 chrY 59373566 210090 0.0035384433537308507 0.11867243205845093