BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084780.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,142,972 number of mapped reads = 1,936,217 (90.35%) number of supplementary alignments = 17,175 (0.8%) number of secondary alignments = 0 number of mapped bases = 130,091,911 bp number of sequenced bases = 130,039,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,895 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9433 >>>>>>> ACTG content number of A's = 36,231,643 bp (27.86%) number of C's = 24,313,677 bp (18.7%) number of T's = 40,730,583 bp (31.32%) number of G's = 28,724,530 bp (22.09%) number of N's = 39,326 bp (0.03%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,104,326 number of insertions = 10,228 mapped reads with insertion percentage = 0.52% number of deletions = 32,068 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.042X std coverageData = 0.3525X There is a 3.62% of reference with a coverageData >= 1X There is a 0.44% 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 11167694 0.04480507994401346 0.555746639325767 chr2 243199373 11331521 0.04659354528845763 0.4310770033338829 chr3 198022430 9488400 0.04791578408567151 0.2457536062185435 chr4 191154276 7015613 0.03670131344589958 0.23191839948963694 chr5 180915260 7516800 0.041548733921063376 0.23057859542216766 chr6 171115067 6687563 0.0390822568535125 0.25757918959704307 chr7 159138663 7394681 0.046466904148867956 0.4571091578368499 chr8 146364022 5492958 0.03752942782619079 0.3541067512221634 chr9 141213431 5337910 0.03780029960464596 0.34117003562254816 chr10 135534747 6105821 0.045049857214843954 0.3191629004145327 chr11 135006516 5981713 0.044306846641387294 0.3406011555429221 chr12 133851895 6322666 0.04723628305747931 0.24768445071987055 chr13 115169878 4235081 0.0367724710101716 0.2173300473055147 chr14 107349540 4204268 0.039164285193956115 0.24913013279463667 chr15 102531392 3888980 0.0379296518279982 0.2252320948524371 chr16 90354753 3885426 0.043001899413083446 0.27392547429822056 chr17 81195210 3720736 0.04582457511964068 0.2910009178269701 chr18 78077248 3222195 0.04126932086540755 0.7970869226404893 chr19 59128983 2689586 0.04548676238859038 0.4232133183853938 chr20 63025520 2963482 0.04702034985193299 0.26200111387673697 chr21 48129895 1863636 0.038720965420763954 0.23256440650200536 chr22 51304566 1594677 0.03108255510825294 0.19692276233792647 chrMT 16571 31930 1.9268601774183816 1.7316537184235765 chrX 155270560 7630312 0.04914203954696885 0.2812061233204296 chrY 59373566 318262 0.005360331565734152 0.1208825114307261