BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240039.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 = 2,451,896 number of mapped reads = 1,871,568 (76.33%) number of supplementary alignments = 9,193 (0.37%) number of secondary alignments = 0 number of mapped bases = 118,582,324 bp number of sequenced bases = 118,527,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,380 duplication rate = 7.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2686 >>>>>>> ACTG content number of A's = 32,716,989 bp (27.6%) number of C's = 21,167,871 bp (17.86%) number of T's = 38,021,665 bp (32.08%) number of G's = 26,536,265 bp (22.39%) number of N's = 84,498 bp (0.07%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,048,218 number of insertions = 7,730 mapped reads with insertion percentage = 0.41% number of deletions = 32,362 mapped reads with deletion percentage = 1.71% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3506X There is a 2.75% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 9261005 0.037155393887664576 0.4488762855377028 chr2 243199373 11725857 0.04821499683718346 0.539519634563133 chr3 198022430 11306241 0.0570957593036304 0.31948398352484886 chr4 191154276 5738461 0.0300200504015929 0.23541902761492015 chr5 180915260 5241100 0.028969916633898102 0.2271145399923331 chr6 171115067 4641834 0.027126974154765695 0.2722983083536306 chr7 159138663 12364679 0.07769751716463774 0.5632181737654955 chr8 146364022 6940798 0.047421476296955 0.3880052046061687 chr9 141213431 3087565 0.021864527886161198 0.33229085947897535 chr10 135534747 4138638 0.03053562345897912 0.3691871233783829 chr11 135006516 8371427 0.06200757747129776 0.4000967113472932 chr12 133851895 5448279 0.040703786823488755 0.27413741379090095 chr13 115169878 4270502 0.037080025386499064 0.25457146547991566 chr14 107349540 2637390 0.024568246869059708 0.21402854586142123 chr15 102531392 2186799 0.021328092375845244 0.20302062529038306 chr16 90354753 2091394 0.02314647465197542 0.20833322730164694 chr17 81195210 2221264 0.027357081778592605 0.2551992717886223 chr18 78077248 1934350 0.02477482300605677 0.36851763877036875 chr19 59128983 1748408 0.029569390699650627 0.31658793997636414 chr20 63025520 6735186 0.1068644257119973 0.44067098960024764 chr21 48129895 1347939 0.028006273439823627 0.22755510316030816 chr22 51304566 748637 0.014592015065481696 0.1546450242581014 chrMT 16571 17940 1.0826142055397985 1.5119906358220705 chrX 155270560 4152872 0.026746036080503605 0.23656037513232528 chrY 59373566 223759 0.0037686636507566346 0.08635300165841672