BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237300.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 = 2,562,934 number of mapped reads = 2,228,881 (86.97%) number of supplementary alignments = 26,133 (1.02%) number of secondary alignments = 0 number of mapped bases = 134,835,954 bp number of sequenced bases = 134,755,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 868,968 duplication rate = 21.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1091 >>>>>>> ACTG content number of A's = 34,051,430 bp (25.27%) number of C's = 23,726,260 bp (17.61%) number of T's = 44,533,940 bp (33.05%) number of G's = 32,430,540 bp (24.07%) number of N's = 13,435 bp (0.01%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 999,514 number of insertions = 13,034 mapped reads with insertion percentage = 0.58% number of deletions = 45,640 mapped reads with deletion percentage = 2.02% homopolymer indels = 41.19% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.7916X There is a 1.35% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% 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 10460855 0.04196922341870514 0.6273943549709623 chr2 243199373 8347954 0.03432555724557727 1.526245002185166 chr3 198022430 8741193 0.044142438813623286 0.5246646131909589 chr4 191154276 8993811 0.04705001210645165 0.8306813418586535 chr5 180915260 10118830 0.05593132386952875 0.5877077574573786 chr6 171115067 10771689 0.06294997389096076 0.8108258725082284 chr7 159138663 7008512 0.044040284541035764 0.6040843727905381 chr8 146364022 7921294 0.05412049964027362 1.0813877326675052 chr9 141213431 6164785 0.04365579786812205 0.5984286798046694 chr10 135534747 5144905 0.03796004429771799 1.0364244319144562 chr11 135006516 4333094 0.03209544345252195 0.49524781058022815 chr12 133851895 5067961 0.03786245237693497 0.5154905152109505 chr13 115169878 7168098 0.062239346993143464 0.667743744370862 chr14 107349540 3999546 0.03725722532206473 0.5000859920754062 chr15 102531392 3076228 0.03000279173036098 0.4887686323560809 chr16 90354753 2685299 0.029719510162348625 0.506006764925851 chr17 81195210 4732242 0.058282280444868606 0.6645464756198189 chr18 78077248 2449536 0.03137323692556377 1.1770384972943437 chr19 59128983 2127771 0.03598524601716894 0.521146692730994 chr20 63025520 3120626 0.04951368905801967 0.5952415232086309 chr21 48129895 1705579 0.03543699814844807 0.6461828671789511 chr22 51304566 1227154 0.023919001673262375 0.39362909155737397 chrMT 16571 17004 1.0261299861203308 2.74651586108092 chrX 155270560 8675689 0.05587465518254072 0.6145827842933788 chrY 59373566 776299 0.013074825251358491 0.6366760890236367