BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083644.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 = 1,502,198 number of mapped reads = 1,228,177 (81.76%) number of supplementary alignments = 7,865 (0.52%) number of secondary alignments = 0 number of mapped bases = 75,553,082 bp number of sequenced bases = 75,525,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,755 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5504 >>>>>>> ACTG content number of A's = 22,457,645 bp (29.74%) number of C's = 14,342,768 bp (18.99%) number of T's = 22,265,348 bp (29.48%) number of G's = 16,449,725 bp (21.78%) number of N's = 10,074 bp (0.01%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 669,837 number of insertions = 5,821 mapped reads with insertion percentage = 0.47% number of deletions = 17,155 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.216X There is a 2.27% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6029647 0.024191101212943416 0.38215045890038246 chr2 243199373 6437416 0.02646970640010655 0.2070010159606474 chr3 198022430 5226071 0.026391308297751926 0.1705051884624217 chr4 191154276 5127567 0.026824233845545782 0.17736122214844646 chr5 180915260 4476547 0.024743888381776085 0.16569960140394838 chr6 171115067 4571147 0.026713877860913324 0.18435518385388297 chr7 159138663 4188176 0.026317777974545382 0.2506437580180902 chr8 146364022 3970055 0.027124527911647576 0.2838501664791863 chr9 141213431 3173075 0.022470065188062743 0.18713393910637038 chr10 135534747 3502582 0.025842686672813135 0.21423242247369653 chr11 135006516 3467314 0.02568256779546848 0.18076361916795244 chr12 133851895 3404479 0.025434671657057973 0.16916436243491426 chr13 115169878 2486702 0.021591600539856436 0.15386899110433455 chr14 107349540 2258078 0.021034817662003956 0.15947424658355425 chr15 102531392 2122130 0.020697368470331507 0.15158953624000057 chr16 90354753 1973885 0.021845945392601537 0.16399754422404522 chr17 81195210 1854550 0.022840633086606957 0.16718540425452663 chr18 78077248 2011802 0.02576681493691991 0.29207824313324354 chr19 59128983 1357615 0.022960229165450048 0.28888938144341064 chr20 63025520 1484895 0.023560218146553968 0.16472840132956332 chr21 48129895 1015823 0.02110586362176772 0.15839886479427948 chr22 51304566 771571 0.015039031808591851 0.1285763244665417 chrMT 16571 6439 0.3885703940619154 0.6725294732429078 chrX 155270560 4434912 0.028562478295949986 0.1884444361954446 chrY 59373566 200604 0.003378675284553399 0.09030257080097696