BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068157.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,948,605 number of mapped reads = 4,604,578 (93.05%) number of supplementary alignments = 28,665 (0.58%) number of secondary alignments = 0 number of mapped bases = 296,360,407 bp number of sequenced bases = 296,232,668 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 484,278 duplication rate = 8.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9595 >>>>>>> ACTG content number of A's = 76,466,769 bp (25.81%) number of C's = 53,576,977 bp (18.09%) number of T's = 96,206,774 bp (32.48%) number of G's = 69,948,558 bp (23.61%) number of N's = 33,590 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,621,665 number of insertions = 18,115 mapped reads with insertion percentage = 0.39% number of deletions = 73,131 mapped reads with deletion percentage = 1.57% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.0957X std coverageData = 1.2265X There is a 7.3% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 37916432 0.1521217152754857 3.3121860539742545 chr2 243199373 25312299 0.10408044514160816 1.6517641967023047 chr3 198022430 21705899 0.10961333521662167 0.4158813029960337 chr4 191154276 14879177 0.07783857788250576 0.37800062478693397 chr5 180915260 14349533 0.07931632190673137 0.3612949432707166 chr6 171115067 13446412 0.07858111056929896 0.5586503003603851 chr7 159138663 27550063 0.1731198596283293 1.4277151022157186 chr8 146364022 12806445 0.08749721977440604 0.9487251371687714 chr9 141213431 12859989 0.09106774694823469 0.6966289829149517 chr10 135534747 12823248 0.09461225467149026 0.5894343278553694 chr11 135006516 15184859 0.11247500824330582 0.6237142438733663 chr12 133851895 11965121 0.08939074788593766 0.4055836592055532 chr13 115169878 6598385 0.05729262819918937 0.35176066630886016 chr14 107349540 4041670 0.03764962569937421 0.31936958763118906 chr15 102531392 6523598 0.06362537241277286 0.3778912325243399 chr16 90354753 4491226 0.04970658267418428 0.35566166525311904 chr17 81195210 8603464 0.10596024075804472 0.45986355433729553 chr18 78077248 6073357 0.077786514709125 1.2991206673482893 chr19 59128983 7841616 0.13261882079047427 1.8364203706196913 chr20 63025520 5212199 0.08269981747076423 0.3915858805072951 chr21 48129895 4120603 0.08561421129217091 0.38319869696009023 chr22 51304566 3824335 0.07454180588916784 0.3376597057100322 chrMT 16571 146642 8.849315068493151 5.553396499784508 chrX 155270560 17504942 0.11273831948567713 0.5225408350691003 chrY 59373566 578893 0.009750012320297555 0.2632347825248359