BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,380,451 number of mapped reads = 1,265,275 (91.66%) number of supplementary alignments = 4,974 (0.36%) number of secondary alignments = 0 number of mapped bases = 72,794,811 bp number of sequenced bases = 72,775,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,214 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4161 >>>>>>> ACTG content number of A's = 17,355,691 bp (23.85%) number of C's = 14,096,909 bp (19.37%) number of T's = 22,775,682 bp (31.3%) number of G's = 18,545,160 bp (25.48%) number of N's = 1,605 bp (0%) GC percentage = 44.85% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 359,291 number of insertions = 4,673 mapped reads with insertion percentage = 0.37% number of deletions = 11,537 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.1935X There is a 2.16% of reference with a coverageData >= 1X There is a 0.14% 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 8134821 0.03263711427222482 0.2753350650192229 chr2 243199373 6075367 0.024981014239703652 0.21108830959815636 chr3 198022430 4745906 0.023966507228499318 0.16538585178962106 chr4 191154276 4621290 0.02417570821172737 0.175867025812037 chr5 180915260 3724530 0.020587152239120127 0.15482640020008587 chr6 171115067 3841252 0.022448356344914967 0.16740810836046066 chr7 159138663 3145952 0.019768621532279682 0.17701309126349535 chr8 146364022 4585390 0.03132866900856277 0.20735768178845063 chr9 141213431 2638773 0.018686416591634263 0.18610210113877482 chr10 135534747 3423912 0.02526224511268686 0.21168130196411344 chr11 135006516 2978755 0.022063786906403836 0.20012441039743653 chr12 133851895 3284272 0.024536611902281995 0.1676696852571439 chr13 115169878 2229566 0.01935893341833704 0.1475998709325434 chr14 107349540 1981673 0.018460004579432757 0.15467579671401177 chr15 102531392 2083917 0.02032467285726502 0.15156851010165032 chr16 90354753 2144412 0.023733250645928943 0.17608657115864718 chr17 81195210 1680926 0.020702280343877427 0.15889300030374603 chr18 78077248 1783457 0.022842211344334267 0.32933560298319253 chr19 59128983 1376360 0.023277247978372974 0.21032049771790226 chr20 63025520 2206944 0.03501667261134855 0.2055676940152939 chr21 48129895 935969 0.019446728483409323 0.16246150016379307 chr22 51304566 873942 0.017034390272397976 0.13914449786869543 chrMT 16571 3437 0.2074105364793917 0.44531570379193985 chrX 155270560 4089543 0.02633817383024831 0.18811348738678518 chrY 59373566 204445 0.0034433673732852765 0.08355648159011422