BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008792.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 = 1,420,886 number of mapped reads = 1,260,382 (88.7%) number of supplementary alignments = 11,269 (0.79%) number of secondary alignments = 0 number of mapped bases = 84,473,287 bp number of sequenced bases = 84,437,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,187 duplication rate = 7.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0654 >>>>>>> ACTG content number of A's = 23,459,258 bp (27.78%) number of C's = 15,526,998 bp (18.39%) number of T's = 26,901,177 bp (31.86%) number of G's = 18,520,675 bp (21.93%) number of N's = 29,087 bp (0.03%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 649,233 number of insertions = 6,430 mapped reads with insertion percentage = 0.51% number of deletions = 20,256 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.3104X There is a 1.73% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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 7070154 0.028365642467145548 0.3515307284969391 chr2 243199373 7469889 0.030715083299166238 0.3283587838178842 chr3 198022430 6959950 0.03514728104285964 0.2769573959480876 chr4 191154276 4282005 0.02240078061345591 0.235611086747795 chr5 180915260 3705395 0.020481384489069634 0.20897267314568305 chr6 171115067 3498253 0.02044386307606682 0.21708502873163615 chr7 159138663 4471574 0.02809860228623386 0.3609248292119263 chr8 146364022 7117646 0.0486297513742824 0.6704076164954145 chr9 141213431 2537387 0.017968453723073975 0.2697489877853454 chr10 135534747 5347979 0.03945836118320271 0.33106633068275 chr11 135006516 2949192 0.02184481229039345 0.2613480915514795 chr12 133851895 3282362 0.02452234239941093 0.22977774217244354 chr13 115169878 2211349 0.019200758378853194 0.20226430634059556 chr14 107349540 3344850 0.03115849401869817 0.2658401020763651 chr15 102531392 2559786 0.024965875816842512 0.230301063472503 chr16 90354753 2424597 0.026834194322904077 0.24520278077491334 chr17 81195210 1969084 0.024251233539515447 0.23347970900364431 chr18 78077248 1267795 0.01623770089847429 0.4014366068991122 chr19 59128983 1845544 0.031212172210031076 0.2952446554158146 chr20 63025520 1958266 0.031071001080197357 0.26442881875005775 chr21 48129895 821429 0.017066918596020206 0.1974433580599356 chr22 51304566 1095970 0.021362036275679633 0.2090332691401931 chrMT 16571 6974 0.4208557117856496 1.0446550810680635 chrX 155270560 6048137 0.0389522456800568 0.32788312684377247 chrY 59373566 227720 0.0038353768409328825 0.11237263890079595