BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085100.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,034,068 number of mapped reads = 1,634,090 (80.34%) number of supplementary alignments = 7,361 (0.36%) number of secondary alignments = 0 number of mapped bases = 99,382,308 bp number of sequenced bases = 99,352,081 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,685 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8922 >>>>>>> ACTG content number of A's = 29,769,371 bp (29.96%) number of C's = 19,314,627 bp (19.44%) number of T's = 28,837,855 bp (29.03%) number of G's = 21,428,304 bp (21.57%) number of N's = 1,924 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 860,258 number of insertions = 7,213 mapped reads with insertion percentage = 0.44% number of deletions = 19,015 mapped reads with deletion percentage = 1.15% homopolymer indels = 45.73% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.2461X There is a 2.86% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 7783608 0.031228038545187818 0.3322022078458825 chr2 243199373 11162240 0.04589748675051066 0.2702362744145858 chr3 198022430 7594800 0.03835323099509485 0.2162558079272395 chr4 191154276 5821336 0.030453600734518752 0.19454865305381905 chr5 180915260 4763376 0.026329321252391867 0.17632489832904596 chr6 171115067 8162384 0.04770114136121047 0.28929383941106124 chr7 159138663 9558484 0.060063870211100115 0.2927215381297923 chr8 146364022 5710033 0.039012545036511775 0.4364745477124677 chr9 141213431 4154209 0.029417945379430658 0.21342951864285573 chr10 135534747 7308647 0.053924526084812775 0.35508060682233944 chr11 135006516 3367308 0.024941818363789198 0.1865680828345593 chr12 133851895 2723360 0.02034606981096532 0.15693916432208535 chr13 115169878 1376949 0.011955808444982462 0.11743538345963446 chr14 107349540 2700551 0.025156614550933334 0.17872376903009796 chr15 102531392 1542410 0.015043295228060494 0.1330674021983025 chr16 90354753 2147034 0.02376226959526966 0.17650056616011592 chr17 81195210 1960022 0.024139625970546783 0.17775127254036432 chr18 78077248 2067287 0.026477457299724498 0.2761070029006348 chr19 59128983 1373295 0.023225412146865437 0.246516867724677 chr20 63025520 1435937 0.022783421699654364 0.16634355618514773 chr21 48129895 748412 0.015549836541301409 0.14380816822622666 chr22 51304566 500413 0.009753771233538941 0.10617032144151368 chrMT 16571 8465 0.5108321766942249 0.830403739737473 chrX 155270560 5204719 0.03352032091595471 0.20766187824173105 chrY 59373566 207029 0.003486888424387378 0.08203244851595974