BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,232,192 number of mapped reads = 1,111,921 (90.24%) number of supplementary alignments = 4,677 (0.38%) number of secondary alignments = 0 number of mapped bases = 63,323,948 bp number of sequenced bases = 63,307,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,857 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1632 >>>>>>> ACTG content number of A's = 16,103,486 bp (25.44%) number of C's = 12,776,502 bp (20.18%) number of T's = 19,339,391 bp (30.55%) number of G's = 15,087,204 bp (23.83%) number of N's = 1,305 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 307,735 number of insertions = 3,135 mapped reads with insertion percentage = 0.28% number of deletions = 9,451 mapped reads with deletion percentage = 0.84% homopolymer indels = 42.12% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.179X There is a 1.89% of reference with a coverageData >= 1X There is a 0.12% 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 7008482 0.028118212792737636 0.25560400827921387 chr2 243199373 5245998 0.021570771072670487 0.20426230236559714 chr3 198022430 4073548 0.020571144390057226 0.15246191134073686 chr4 191154276 4095325 0.021424187236073127 0.1627970784176286 chr5 180915260 3606692 0.019935808621119083 0.1514079985202128 chr6 171115067 3293575 0.019247720599612658 0.1548854671095968 chr7 159138663 3104420 0.019507641584245308 0.16496557772456139 chr8 146364022 3969277 0.02711921239770249 0.19301945541635068 chr9 141213431 2261874 0.016017414094272663 0.17197130446288464 chr10 135534747 3209131 0.023677551853179022 0.1951770452742646 chr11 135006516 2335658 0.017300335340851253 0.1703504195527635 chr12 133851895 3296751 0.024629841811354258 0.168612740185765 chr13 115169878 1055394 0.009163802361586247 0.1007899024349835 chr14 107349540 1606193 0.014962271845785273 0.13705894201213012 chr15 102531392 1813926 0.017691420789449536 0.14207773879112756 chr16 90354753 1900154 0.02102992855284547 0.1608399534906196 chr17 81195210 1693646 0.020858939831549177 0.15666033664554438 chr18 78077248 2207185 0.028269246887390295 0.31188911594783497 chr19 59128983 1005604 0.017006955793574193 0.19843057739591896 chr20 63025520 1348118 0.021390033751407366 0.15794493786725508 chr21 48129895 799529 0.016611899942852566 0.1463941055367812 chr22 51304566 737587 0.01437663462546394 0.12686846972737845 chrMT 16571 13869 0.836944058898075 0.9768740732511021 chrX 155270560 3462171 0.02229766544282445 0.17182731182273248 chrY 59373566 179841 0.0030289742071412723 0.07540162127416565