BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234090.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 = 2,105,783 number of mapped reads = 1,392,727 (66.14%) number of supplementary alignments = 20,811 (0.99%) number of secondary alignments = 0 number of mapped bases = 88,361,884 bp number of sequenced bases = 88,305,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,135 duplication rate = 9.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5014 >>>>>>> ACTG content number of A's = 24,255,946 bp (27.47%) number of C's = 16,448,108 bp (18.63%) number of T's = 27,721,276 bp (31.39%) number of G's = 19,868,539 bp (22.5%) number of N's = 12,099 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 787,674 number of insertions = 6,977 mapped reads with insertion percentage = 0.5% number of deletions = 32,329 mapped reads with deletion percentage = 2.28% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.3023X There is a 1.8% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.09% 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% 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 8856993 0.035534487193915554 0.4234322919641531 chr2 243199373 9054572 0.037231066381079855 0.38932594841974444 chr3 198022430 10165544 0.05133531590335499 0.3389611635747756 chr4 191154276 5014347 0.02623193739071785 0.24947334620600736 chr5 180915260 6390717 0.035324366778125844 0.27881141212989635 chr6 171115067 4923815 0.028774876966269722 0.2977161834778926 chr7 159138663 5649968 0.03550342759886075 0.3263887521492429 chr8 146364022 5618054 0.038384118741967885 0.45033668590536374 chr9 141213431 4640069 0.032858552951666474 0.29362971340047106 chr10 135534747 2798657 0.020649000067857137 0.2955995315549671 chr11 135006516 1949134 0.01443733278770041 0.18498923935184625 chr12 133851895 3286395 0.02455247271620622 0.23518511697454514 chr13 115169878 4443032 0.03857807333962792 0.29680650160702826 chr14 107349540 3278483 0.03054026128104508 0.26868530159490617 chr15 102531392 415236 0.004049842608203349 0.08611101396098293 chr16 90354753 1786361 0.01977052607293387 0.21494746773480045 chr17 81195210 2034215 0.025053386769983105 0.23461989363056115 chr18 78077248 543430 0.006960158226888325 0.3210785399416393 chr19 59128983 1758977 0.029748135529406958 0.31245258029922396 chr20 63025520 2301603 0.03651858802592981 0.29022362356559256 chr21 48129895 1583025 0.03289068052195003 0.2736449548038444 chr22 51304566 758813 0.014790359984723387 0.1768825514611035 chrMT 16571 41079 2.478969283688371 2.7249335726885295 chrX 155270560 856906 0.005518792487126987 0.10565851025176586 chrY 59373566 212459 0.0035783432647451224 0.11605400730203068