BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714136.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 664,782 number of mapped reads = 578,799 (87.07%) number of supplementary alignments = 16,971 (2.55%) number of secondary alignments = 0 number of mapped bases = 75,478,820 bp number of sequenced bases = 73,805,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 517,767 duplication rate = 44.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6873 >>>>>>> ACTG content number of A's = 19,679,685 bp (26.66%) number of C's = 16,682,673 bp (22.6%) number of T's = 18,676,484 bp (25.3%) number of G's = 18,766,499 bp (25.43%) number of N's = 598 bp (0%) GC percentage = 48.03% >>>>>>> Mismatches and indels general error rate = 0.0438 number of mismatches = 3,022,549 number of insertions = 78,577 mapped reads with insertion percentage = 13.07% number of deletions = 266,983 mapped reads with deletion percentage = 43.88% homopolymer indels = 29.92% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 6.3381X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6660432 0.026721827104294354 6.828160485735123 chr2 243199373 9370810 0.03853139045716208 10.584669262448932 chr3 198022430 2353035 0.011882669049157715 2.2501246534965946 chr4 191154276 2436252 0.012744951622217438 2.5860612344843363 chr5 180915260 3996384 0.022089811550446325 3.944006391179809 chr6 171115067 2929930 0.01712257167862372 3.2487798961032075 chr7 159138663 2159815 0.013571906155828392 2.2306225330034795 chr8 146364022 2725939 0.018624378879120992 3.85475909017948 chr9 141213431 3749780 0.02655398975469975 6.780992645427152 chr10 135534747 3469386 0.025597760550657905 3.9394762601034476 chr11 135006516 3355238 0.02485241527157104 4.462800833992921 chr12 133851895 4178011 0.03121368584284892 8.020388930897292 chr13 115169878 2700857 0.023451071121217998 7.04230876867119 chr14 107349540 4119647 0.03837600980870528 18.177286760658493 chr15 102531392 2950415 0.02877572363398714 5.484236330688372 chr16 90354753 1245618 0.013785860274555783 1.8303846025116135 chr17 81195210 2676243 0.03296060198625017 5.715089525269707 chr18 78077248 2285280 0.02926947425196134 6.312307864354627 chr19 59128983 1884495 0.031870918530765194 3.3082243285083583 chr20 63025520 1856987 0.029464048848783793 3.679416938892366 chr21 48129895 766953 0.015935064890542562 3.013720060205016 chr22 51304566 446700 0.008706827380627292 1.0003215512978156 chrMT 16571 173077 10.444571842375234 86.6666698327816 chrX 155270560 6405218 0.04125197977002208 4.354691180563789 chrY 59373566 582318 0.009807697924022283 2.3863923841427925