BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013254.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,169,729 number of mapped reads = 1,939,351 (89.38%) number of supplementary alignments = 14,849 (0.68%) number of secondary alignments = 0 number of mapped bases = 130,393,577 bp number of sequenced bases = 130,332,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,726 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8438 >>>>>>> ACTG content number of A's = 36,441,214 bp (27.96%) number of C's = 23,858,439 bp (18.31%) number of T's = 41,588,622 bp (31.91%) number of G's = 28,442,748 bp (21.82%) number of N's = 1,790 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 941,854 number of insertions = 9,842 mapped reads with insertion percentage = 0.5% number of deletions = 35,273 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.3686X There is a 3.45% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% 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 7633227 0.03062470604636929 0.39630940497063 chr2 243199373 18055209 0.07424035998645441 0.5075512154173545 chr3 198022430 6254484 0.03158472502332185 0.2074736792395342 chr4 191154276 7187614 0.03760111544666676 0.2598903530482488 chr5 180915260 7580914 0.04190312083126653 0.24076621181402663 chr6 171115067 6449514 0.03769109356103633 0.28788453223993654 chr7 159138663 5706447 0.03585833192528456 0.5584051883557538 chr8 146364022 9860441 0.06736929516736019 0.5117041254847398 chr9 141213431 3209403 0.022727321171029404 0.3288127044751052 chr10 135534747 7786979 0.05745374652892516 0.4376250297558391 chr11 135006516 9030700 0.06689084547593244 0.5410127442119588 chr12 133851895 8836814 0.06601934175082093 0.30320129562129416 chr13 115169878 1799568 0.015625335645488833 0.14531399588222094 chr14 107349540 6192833 0.05768849125948747 0.2904935477216191 chr15 102531392 2498939 0.0243724282998128 0.1898931122224172 chr16 90354753 3221289 0.035651572197867666 0.24920939960309157 chr17 81195210 3157633 0.03888940000278342 0.2975259628385051 chr18 78077248 3376702 0.043248220019230184 0.6885248938505659 chr19 59128983 2036908 0.034448554611534586 0.3360995099106464 chr20 63025520 2007537 0.03185276376934296 0.21454223064672046 chr21 48129895 1938387 0.04027407497980205 0.25639555733837155 chr22 51304566 1456588 0.02839100129996227 0.19294711417558816 chrMT 16571 14143 0.8534789692836884 1.294331945589085 chrX 155270560 4839885 0.03117065463021451 0.2557578189252567 chrY 59373566 261419 0.0044029526540480994 0.1271385640044691