BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004139.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 = 2,079,547 number of mapped reads = 1,856,916 (89.29%) number of supplementary alignments = 16,702 (0.8%) number of secondary alignments = 0 number of mapped bases = 120,158,343 bp number of sequenced bases = 120,098,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,373 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.356 >>>>>>> ACTG content number of A's = 33,280,447 bp (27.71%) number of C's = 22,435,126 bp (18.68%) number of T's = 36,060,118 bp (30.03%) number of G's = 28,298,777 bp (23.56%) number of N's = 24,338 bp (0.02%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,061,886 number of insertions = 10,879 mapped reads with insertion percentage = 0.58% number of deletions = 35,350 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3902X There is a 3.52% of reference with a coverageData >= 1X There is a 0.22% 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 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9766534 0.03918358943627266 0.7515046485152733 chr2 243199373 9547359 0.039257333940577226 0.4188110705889168 chr3 198022430 7812504 0.039452621604532376 0.2131721317554114 chr4 191154276 7726317 0.040419273697021564 0.24475562262147 chr5 180915260 6636558 0.036683240540350215 0.20918616322565464 chr6 171115067 7024386 0.041050657450287534 0.25151317793341077 chr7 159138663 7509566 0.04718882173843574 0.5444639492352579 chr8 146364022 7248942 0.04952680242689696 0.4213966520932247 chr9 141213431 4704002 0.03331129317295605 0.3694356835677626 chr10 135534747 5744275 0.04238230510733901 0.4104257153953435 chr11 135006516 5412906 0.04009366481244505 0.31944286898839713 chr12 133851895 5469124 0.04085951864932506 0.22084245362136135 chr13 115169878 3768095 0.032717712872805164 0.1917539937926143 chr14 107349540 3100487 0.028882163817376395 0.23455466662947166 chr15 102531392 3296389 0.03215004629996636 0.1930201372014604 chr16 90354753 3201631 0.035434007550217084 0.25320525358853846 chr17 81195210 3193955 0.03933674166246999 0.23952377629686672 chr18 78077248 3432464 0.0439624101505217 0.6850978611998619 chr19 59128983 2427212 0.04104944608974587 0.5242849847836549 chr20 63025520 2681308 0.042543211067516774 0.24317669780767748 chr21 48129895 1517863 0.03153680264625551 0.2245417267550881 chr22 51304566 1375976 0.026819757134287033 0.17215956078491434 chrMT 16571 427823 25.817572868263834 17.161765881178574 chrX 155270560 6767247 0.043583580815320044 0.26064660788297683 chrY 59373566 365420 0.006154590748347505 0.16172074898645028