BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068154.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 = 3,984,320 number of mapped reads = 3,762,574 (94.43%) number of supplementary alignments = 29,152 (0.73%) number of secondary alignments = 0 number of mapped bases = 242,277,481 bp number of sequenced bases = 242,171,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,297,601 duplication rate = 20.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6278 >>>>>>> ACTG content number of A's = 63,258,876 bp (26.12%) number of C's = 43,092,528 bp (17.79%) number of T's = 79,628,301 bp (32.88%) number of G's = 56,164,669 bp (23.19%) number of N's = 27,331 bp (0.01%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,292,917 number of insertions = 15,429 mapped reads with insertion percentage = 0.41% number of deletions = 59,275 mapped reads with deletion percentage = 1.56% homopolymer indels = 47.24% >>>>>>> Coverage mean coverageData = 0.0783X std coverageData = 0.913X There is a 2.17% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.59% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 24353979 0.09770879969041281 1.1272543941564328 chr2 243199373 22685507 0.09327946334795854 1.266195960799763 chr3 198022430 15851025 0.08004661391136347 0.740276329254974 chr4 191154276 15517862 0.08117977962470481 0.7405934740777449 chr5 180915260 12064533 0.06668609933733617 0.6678547050222268 chr6 171115067 12217043 0.07139665263959485 0.7682521319928027 chr7 159138663 25230873 0.15854646837142272 1.2104999061873138 chr8 146364022 7705354 0.05264513706790594 1.717397614537004 chr9 141213431 6040623 0.04277654722517152 0.6116163129836476 chr10 135534747 11344324 0.08370048457020397 0.8022983005098692 chr11 135006516 18693706 0.13846521304201348 0.9761235053474143 chr12 133851895 9120708 0.06814029790164719 0.6948070077843199 chr13 115169878 4322905 0.037535031512319565 0.5269577257275979 chr14 107349540 5778551 0.053829303786490375 0.6042167055784903 chr15 102531392 4238179 0.04133542827546904 0.5498312451122386 chr16 90354753 4165341 0.04609985486873059 0.5715273859724517 chr17 81195210 9472991 0.11666933308011643 0.8503195206867241 chr18 78077248 4997567 0.0640079809165405 0.9255239292793854 chr19 59128983 4885000 0.08261599899325175 0.9014873143712775 chr20 63025520 2972100 0.04715708811287872 0.5769198875450677 chr21 48129895 3185895 0.06619368274125675 0.6873626638864693 chr22 51304566 2065224 0.040254194919025335 0.5398680745432485 chrMT 16571 396202 23.90935972482047 17.6383309277435 chrX 155270560 14160218 0.09119705628678096 0.7708484724961793 chrY 59373566 811771 0.013672262838314277 0.3340041163140177