BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063591.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 = 5,946,598 number of mapped reads = 5,372,266 (90.34%) number of supplementary alignments = 39,577 (0.67%) number of secondary alignments = 0 number of mapped bases = 360,551,617 bp number of sequenced bases = 360,362,390 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,271 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8292 >>>>>>> ACTG content number of A's = 103,096,221 bp (28.61%) number of C's = 66,382,862 bp (18.42%) number of T's = 112,478,541 bp (31.21%) number of G's = 78,206,309 bp (21.7%) number of N's = 198,457 bp (0.06%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,184,721 number of insertions = 29,511 mapped reads with insertion percentage = 0.54% number of deletions = 113,794 mapped reads with deletion percentage = 2.09% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.1165X std coverageData = 0.9768X There is a 9.45% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 23061942 0.09252511350814248 1.9039921784827805 chr2 243199373 33133072 0.1362383117657133 1.1074178934232275 chr3 198022430 20676468 0.1044147776592783 0.3818167661340764 chr4 191154276 26337360 0.13778064792021708 0.4781031048946594 chr5 180915260 22372144 0.12366090068908504 0.4216414644770502 chr6 171115067 24271830 0.1418450778504502 0.579165526508114 chr7 159138663 21480899 0.13498227643146657 1.4108527646503308 chr8 146364022 22217141 0.15179373111241778 1.6533524465056295 chr9 141213431 14847225 0.10514031770816475 0.8969502288987575 chr10 135534747 16326823 0.12046226787880454 0.8265256280376687 chr11 135006516 18513231 0.13712842571243006 0.8963511369043218 chr12 133851895 18320402 0.13687069577909225 0.45757925203888494 chr13 115169878 9971557 0.08658129341771119 0.34122362019553076 chr14 107349540 10441141 0.09726302506745721 0.4771150018643134 chr15 102531392 8585183 0.08373223880545774 0.35748644382031475 chr16 90354753 10539985 0.11665114064337047 0.5549953202414403 chr17 81195210 7972236 0.09818603831432914 0.48772320244322787 chr18 78077248 10608554 0.1358725399747696 1.755173193643799 chr19 59128983 5564936 0.09411519897103592 1.3518864775717805 chr20 63025520 8361291 0.13266516484116275 0.4730722263768853 chr21 48129895 4749777 0.09868662709528038 0.434747840224871 chr22 51304566 2671235 0.0520662235014326 0.2583414421127503 chrMT 16571 213066 12.857763562850764 7.639627166338972 chrX 155270560 18450992 0.11883123239846627 0.5456051583912445 chrY 59373566 863127 0.014537226886456507 0.28484002884844783