BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080919.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 = 3,566,974 number of mapped reads = 3,213,699 (90.1%) number of supplementary alignments = 40,068 (1.12%) number of secondary alignments = 0 number of mapped bases = 223,042,111 bp number of sequenced bases = 222,960,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,507 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9344 >>>>>>> ACTG content number of A's = 64,908,144 bp (29.11%) number of C's = 39,948,217 bp (17.92%) number of T's = 70,772,667 bp (31.74%) number of G's = 46,238,589 bp (20.74%) number of N's = 1,093,217 bp (0.49%) GC percentage = 38.66% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 2,519,792 number of insertions = 17,031 mapped reads with insertion percentage = 0.53% number of deletions = 49,305 mapped reads with deletion percentage = 1.52% homopolymer indels = 50.44% >>>>>>> Coverage mean coverageData = 0.072X std coverageData = 0.4733X There is a 5.27% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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% 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 17494682 0.07018912101326319 0.7526171301364808 chr2 243199373 19416556 0.07983801833239101 0.47466921475096624 chr3 198022430 15888637 0.08023655199060026 0.36513184162464346 chr4 191154276 15974301 0.08356758391321573 0.38737614495406375 chr5 180915260 14427249 0.07974589318778305 0.36618531051636666 chr6 171115067 13849539 0.0809369931170351 0.4239272975937926 chr7 159138663 12123892 0.07618445305148756 0.5783140118831163 chr8 146364022 11855991 0.08100345179090528 0.7626952689574181 chr9 141213431 9702057 0.06870491660244414 0.4395134770514571 chr10 135534747 10036138 0.07404845046857246 0.43794553725659074 chr11 135006516 10365720 0.07677940522515224 0.42971530077707815 chr12 133851895 9763825 0.07294498893721303 0.352359854003904 chr13 115169878 7384070 0.06411459426917167 0.32888546606863517 chr14 107349540 6738391 0.06277056240762653 0.3395368276369185 chr15 102531392 6162459 0.06010314382545397 0.3167253520608951 chr16 90354753 5253523 0.058143294354420956 0.33389703591126024 chr17 81195210 4814229 0.05929203212849625 0.3395085447154937 chr18 78077248 5888293 0.07541624674066381 0.7238434857880299 chr19 59128983 3196785 0.05406460314056137 0.5124848145694659 chr20 63025520 3912816 0.062083041916988546 0.329587828040249 chr21 48129895 2896967 0.06019059463977638 0.34698107094302594 chr22 51304566 2006656 0.03911262011260362 0.2509938634233962 chrMT 16571 119826 7.231066320680707 4.276910874840374 chrX 155270560 13298149 0.0856450121645726 0.39503999040438287 chrY 59373566 471360 0.007938886473485524 0.15442081556725984