BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083778.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 = 2,138,554 number of mapped reads = 1,275,071 (59.62%) number of supplementary alignments = 6,859 (0.32%) number of secondary alignments = 0 number of mapped bases = 81,256,141 bp number of sequenced bases = 81,229,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,028 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8081 >>>>>>> ACTG content number of A's = 23,302,803 bp (28.69%) number of C's = 15,207,812 bp (18.72%) number of T's = 24,652,430 bp (30.35%) number of G's = 18,065,785 bp (22.24%) number of N's = 905 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 681,760 number of insertions = 5,773 mapped reads with insertion percentage = 0.45% number of deletions = 16,732 mapped reads with deletion percentage = 1.3% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.2089X There is a 2.39% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 6481652 0.026004557075907948 0.27547996287472964 chr2 243199373 7009578 0.028822352268153256 0.25798219377738735 chr3 198022430 5626553 0.02841371555737398 0.1814180110232232 chr4 191154276 5382686 0.028158857403744398 0.1830174306677488 chr5 180915260 5149836 0.028465459464281785 0.18239278149857027 chr6 171115067 4650012 0.027174766556354736 0.19219566287650186 chr7 159138663 4515724 0.028376033296195282 0.2379162178765242 chr8 146364022 4205474 0.02873297646876635 0.21553347129919845 chr9 141213431 3465810 0.02454306205477013 0.20775150798872863 chr10 135534747 3822518 0.028203232636720088 0.21483903496529516 chr11 135006516 3656517 0.027084003856524968 0.19530321530141098 chr12 133851895 3751561 0.028027701811767402 0.18062415365529286 chr13 115169878 2650066 0.02301006171075392 0.16346962838676507 chr14 107349540 2523478 0.023507115167889867 0.17035529983283068 chr15 102531392 2291482 0.022349077246508073 0.16672184732391113 chr16 90354753 2169491 0.02401081213735375 0.17677446595755797 chr17 81195210 2047197 0.025213273048988974 0.17841371472888312 chr18 78077248 2243053 0.028728638079047047 0.34005657832923364 chr19 59128983 1384221 0.02341019462485935 0.22585657322386232 chr20 63025520 1572340 0.024947671990647596 0.17407399547646646 chr21 48129895 1026279 0.021323109057270955 0.1610697172626204 chr22 51304566 788661 0.01537214056152429 0.13234613449094557 chrMT 16571 18911 1.1412105485486694 1.2848986207275894 chrX 155270560 4627875 0.029805231590586137 0.1979270705103507 chrY 59373566 195166 0.003287085704099363 0.07475063452898678