BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230406.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 = 2,079,398 number of mapped reads = 1,174,964 (56.51%) number of supplementary alignments = 13,312 (0.64%) number of secondary alignments = 0 number of mapped bases = 74,566,555 bp number of sequenced bases = 74,535,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,576 duplication rate = 14.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7397 >>>>>>> ACTG content number of A's = 20,641,605 bp (27.69%) number of C's = 13,740,317 bp (18.43%) number of T's = 23,659,854 bp (31.74%) number of G's = 16,439,192 bp (22.06%) number of N's = 54,135 bp (0.07%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 727,347 number of insertions = 5,585 mapped reads with insertion percentage = 0.47% number of deletions = 19,424 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0241X std coverageData = 0.5213X There is a 0.74% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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% 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 5504298 0.02208338730678629 0.5585317992665264 chr2 243199373 6045779 0.024859352741834578 0.6280301713596383 chr3 198022430 4192736 0.021173035802055352 0.4250844819726733 chr4 191154276 7575628 0.03963096279363377 0.5987667316671806 chr5 180915260 4823653 0.026662499338087897 0.4733378509867061 chr6 171115067 5350939 0.031270998479637095 0.5756482515291961 chr7 159138663 3778260 0.02374193630117403 0.47816009583627583 chr8 146364022 3571150 0.024399097204366248 0.49631947554169664 chr9 141213431 2584952 0.01830528428984917 0.3936185295884114 chr10 135534747 4065307 0.029994574011341903 0.515056931889022 chr11 135006516 3199364 0.023697848776424984 0.4449573907015061 chr12 133851895 3525845 0.026341390235827444 0.48272469781703703 chr13 115169878 2492189 0.021639243205588878 0.47732397993815495 chr14 107349540 2114448 0.019696851984647535 0.7232191211166958 chr15 102531392 1894868 0.018480857062781318 0.8235187275148296 chr16 90354753 2003287 0.02217135162773341 0.4346341378100648 chr17 81195210 1632973 0.02011169131775138 0.41327003809263746 chr18 78077248 1914659 0.02452262405560196 0.4939123954095706 chr19 59128983 1302402 0.022026456974577086 0.4244576984229915 chr20 63025520 1279881 0.02030734534201384 0.39336372373458367 chr21 48129895 952007 0.01977995173270168 0.3932190242764791 chr22 51304566 599259 0.011680422362407275 0.27795122155976815 chrMT 16571 25199 1.5206686379820167 3.958354803259193 chrX 155270560 3940069 0.025375505826732384 0.5191081183184901 chrY 59373566 197403 0.003324762403524828 0.17828498408866922