BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240230.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 = 1,459,360 number of mapped reads = 1,137,955 (77.98%) number of supplementary alignments = 10,458 (0.72%) number of secondary alignments = 0 number of mapped bases = 75,271,433 bp number of sequenced bases = 75,236,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,533 duplication rate = 8.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7385 >>>>>>> ACTG content number of A's = 21,322,520 bp (28.34%) number of C's = 14,020,224 bp (18.63%) number of T's = 23,753,296 bp (31.57%) number of G's = 16,082,599 bp (21.38%) number of N's = 58,134 bp (0.08%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 677,600 number of insertions = 5,337 mapped reads with insertion percentage = 0.47% number of deletions = 20,087 mapped reads with deletion percentage = 1.74% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2973X There is a 1.38% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% 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 0.01% 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 6052223 0.024281676714458418 0.4419426526959482 chr2 243199373 8038508 0.03305316087307511 0.3350052141946345 chr3 198022430 4658243 0.023523814953689843 0.24693094870897436 chr4 191154276 4863790 0.0254443170290368 0.25798982991003827 chr5 180915260 4021265 0.02222734002648533 0.2382003412654084 chr6 171115067 3895881 0.022767609353768946 0.26066064692778895 chr7 159138663 4479699 0.028149658389426083 0.36116688015076776 chr8 146364022 4217681 0.028816378112375186 0.3610596796520759 chr9 141213431 2748421 0.019462886642843485 0.2610594078445214 chr10 135534747 3677180 0.027130902454113853 0.3070635869859027 chr11 135006516 3305673 0.024485284843584882 0.30108466073135637 chr12 133851895 3682589 0.02751241586829981 0.2673681342356691 chr13 115169878 1976343 0.017160242194577995 0.21281556577761732 chr14 107349540 2427659 0.02261452634077426 0.2501977737879449 chr15 102531392 2112010 0.020598666991666317 0.23997253539500235 chr16 90354753 2293710 0.02538560423047142 0.25577514228219217 chr17 81195210 1737474 0.02139872536815903 0.24653907932205701 chr18 78077248 1886972 0.024168013708679895 0.3780393932928186 chr19 59128983 1324296 0.022396732242122276 0.31436828294611646 chr20 63025520 1541882 0.02446440743368718 0.2524361068404501 chr21 48129895 1139360 0.02367260514488968 0.24827292082368743 chr22 51304566 718889 0.014012183632934348 0.1828341626308003 chrMT 16571 16564 0.9995775752821193 1.4739298966968155 chrX 155270560 4229073 0.02723679878529452 0.2759376843464453 chrY 59373566 226048 0.003807216160807993 0.1045775868813475