BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708652.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 22,948,608 number of mapped reads = 22,381,330 (97.53%) number of supplementary alignments = 546 (0%) number of secondary alignments = 0 number of mapped bases = 1,116,542,093 bp number of sequenced bases = 1,116,439,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 248,521 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3242 >>>>>>> ACTG content number of A's = 339,235,774 bp (30.39%) number of C's = 217,269,590 bp (19.46%) number of T's = 337,613,441 bp (30.24%) number of G's = 222,281,949 bp (19.91%) number of N's = 39,189 bp (0%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0022 number of mismatches = 2,317,748 number of insertions = 68,301 mapped reads with insertion percentage = 0.3% number of deletions = 60,498 mapped reads with deletion percentage = 0.27% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.3607X std coverageData = 0.7086X There is a 26.3% of reference with a coverageData >= 1X There is a 7.11% of reference with a coverageData >= 2X There is a 1.9% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 83869519 0.33648670026784006 0.6979208461860036 chr2 243199373 106031724 0.43598683126539145 0.768762209512218 chr3 198022430 83832087 0.4233464209079749 0.7489561797335427 chr4 191154276 93389311 0.48855465310124685 0.8136498511089016 chr5 180915260 75055280 0.4148642850802083 0.7400418883840181 chr6 171115067 73725707 0.4308545605747272 0.7561176880534131 chr7 159138663 61141784 0.3842044594782099 0.7253357182348815 chr8 146364022 65374537 0.4466571504847004 0.7761825508825927 chr9 141213431 43691437 0.30940001025823105 0.6558863531513475 chr10 135534747 49290083 0.36367119200805387 0.6941242917654903 chr11 135006516 53229345 0.39427241422925097 0.7422225559327026 chr12 133851895 54493001 0.40711415404316836 0.7467401597017177 chr13 115169878 40687973 0.353286585924837 0.697383383797869 chr14 107349540 35128380 0.3272336332321499 0.6793404171530918 chr15 102531392 28629139 0.2792231573331219 0.6287382740515741 chr16 90354753 21362076 0.2364244856050904 0.5694246236787175 chr17 81195210 18491388 0.2277398876115968 0.5482737605740508 chr18 78077248 45717392 0.5855405149525762 0.9139002192495371 chr19 59128983 10051052 0.16998519998221515 0.4656727946743514 chr20 63025520 18855128 0.2991665598316365 0.6401715983069918 chr21 48129895 11571980 0.24043227187593075 0.5941124981717184 chr22 51304566 6835631 0.1332363088306799 0.4269316833019038 chrMT 16571 2758 0.16643533884497014 0.41318059321672046 chrX 155270560 31134507 0.2005177736204468 0.5096060601173173 chrY 59373566 4950874 0.08338515493578405 0.34086043667736304