BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,692,433 number of mapped reads = 3,202,507 (86.73%) number of secondary alignments = 0 number of mapped bases = 126,885,581 bp number of sequenced bases = 126,871,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,970 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9217 >>>>>>> ACTG content number of A's = 36,278,078 bp (28.59%) number of C's = 26,707,097 bp (21.05%) number of T's = 36,861,286 bp (29.05%) number of G's = 27,024,242 bp (21.3%) number of N's = 1,129 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 293,899 number of insertions = 3,514 mapped reads with insertion percentage = 0.11% number of deletions = 10,197 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.4147X There is a 3.51% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10281582 0.04124997546144529 0.5107249636133063 chr2 243199373 10889829 0.044777372842980154 0.27985995345094894 chr3 198022430 8783438 0.044355773232355546 0.23927137326114956 chr4 191154276 8274331 0.04328614129458448 0.24410789821661089 chr5 180915260 7966365 0.044033681846406984 0.23827143699055534 chr6 171115067 7432219 0.04343404195961306 0.24046604726891305 chr7 159138663 7141731 0.04487740983471754 0.39891817896416637 chr8 146364022 6642625 0.04538427483223985 1.364708653517274 chr9 141213431 5448703 0.03858487794974686 0.26386743054616857 chr10 135534747 6085754 0.04490179924119385 0.28087689109476977 chr11 135006516 5848041 0.043316731467983365 0.2783365159276913 chr12 133851895 5839270 0.043624858654410535 0.23890656631795704 chr13 115169878 4099407 0.03559443728854171 0.21280546136499864 chr14 107349540 4009470 0.03734967099067216 0.22985565839760003 chr15 102531392 3706726 0.03615210841963406 0.2141801210761505 chr16 90354753 3680619 0.04073520072596513 0.23612102402476456 chr17 81195210 3411688 0.042018340737095206 0.23902858696254645 chr18 78077248 3434515 0.043988679006719086 0.3949776490536898 chr19 59128983 2536321 0.04289471713051449 0.43222836292458844 chr20 63025520 2762277 0.04382791288354305 0.24320302629081306 chr21 48129895 1686282 0.03503606230597428 0.23481232614235817 chr22 51304566 1549434 0.030200703773617343 0.25560537810109457 chrMT 16571 4961 0.29937843220083277 0.6321397978509304 chrX 155270560 4160693 0.026796406221501357 0.2058795980021945 chrY 59373566 1209300 0.020367649805639095 0.25501225575184977