BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971323.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 86,738,332 number of mapped reads = 75,181,671 (86.68%) number of secondary alignments = 0 number of mapped bases = 2,948,858,127 bp number of sequenced bases = 2,948,550,114 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,035,950 duplication rate = 30.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 28.94 >>>>>>> ACTG content number of A's = 793,670,312 bp (26.92%) number of C's = 657,324,278 bp (22.29%) number of T's = 824,022,769 bp (27.95%) number of G's = 673,507,153 bp (22.84%) number of N's = 25,602 bp (0%) GC percentage = 45.14% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 12,656,049 number of insertions = 134,778 mapped reads with insertion percentage = 0.18% number of deletions = 246,699 mapped reads with deletion percentage = 0.33% homopolymer indels = 34.05% >>>>>>> Coverage mean coverageData = 0.9526X std coverageData = 6.7256X There is a 29.52% of reference with a coverageData >= 1X There is a 19.29% of reference with a coverageData >= 2X There is a 12.81% of reference with a coverageData >= 3X There is a 8.72% of reference with a coverageData >= 4X There is a 6.06% of reference with a coverageData >= 5X There is a 4.27% of reference with a coverageData >= 6X There is a 3.05% of reference with a coverageData >= 7X There is a 2.2% of reference with a coverageData >= 8X There is a 1.61% of reference with a coverageData >= 9X There is a 1.19% of reference with a coverageData >= 10X There is a 0.89% of reference with a coverageData >= 11X There is a 0.67% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.4% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% 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 241156874 0.9675276756883185 11.736490582937387 chr2 243199373 244075977 1.0036044665296073 6.53114401666114 chr3 198022430 193365464 0.9764826338107254 2.5710835067920224 chr4 191154276 177526129 0.928706031143138 3.1885121123345854 chr5 180915260 175120488 0.9679696892346173 2.7207362368995094 chr6 171115067 172234504 1.0065420130420193 3.034686138734202 chr7 159138663 168145767 1.0565990930814846 10.21493518213434 chr8 146364022 140872747 0.9624820709012766 12.598473039279808 chr9 141213431 124998301 0.8851728912386528 6.727047790309493 chr10 135534747 139724525 1.0309129436748792 5.52365445712458 chr11 135006516 134457074 0.9959302556922511 5.770711613790458 chr12 133851895 139257683 1.040386338945743 2.985314024442143 chr13 115169878 84657711 0.7350681660008357 2.0122279287919587 chr14 107349540 91762399 0.8548001137219591 4.117776572841877 chr15 102531392 86499767 0.8436417892385583 2.6476117753208923 chr16 90354753 88307106 0.977337694675564 3.3950351141569652 chr17 81195210 91235234 1.1236529100669854 3.041029937153071 chr18 78077248 72329743 0.9263869418143427 13.394904369320457 chr19 59128983 76466571 1.293216407933145 12.84410615543012 chr20 63025520 63590734 1.0089680180345992 3.182933863873546 chr21 48129895 34797164 0.7229844154033579 3.1594251859125295 chr22 51304566 37788645 0.7365552025135541 2.3059333007850595 chrMT 16571 76220 4.599601713837427 5.518100479364318 chrX 155270560 156788211 1.0097742353734025 4.293388100516227 chrY 59373566 13623089 0.22944704045568023 1.970219322437782