BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237264.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 = 2,722,918 number of mapped reads = 2,468,648 (90.66%) number of supplementary alignments = 21,283 (0.78%) number of secondary alignments = 0 number of mapped bases = 171,814,729 bp number of sequenced bases = 171,726,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,597 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.801 >>>>>>> ACTG content number of A's = 50,653,588 bp (29.5%) number of C's = 31,894,955 bp (18.57%) number of T's = 54,099,019 bp (31.5%) number of G's = 35,075,998 bp (20.43%) number of N's = 3,093 bp (0%) GC percentage = 39% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,340,847 number of insertions = 12,064 mapped reads with insertion percentage = 0.48% number of deletions = 50,558 mapped reads with deletion percentage = 2.02% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.0555X std coverageData = 0.6402X There is a 3.34% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 24827175 0.09960727439872658 1.3293571121640104 chr2 243199373 6805756 0.027984266225883733 0.5822015018440655 chr3 198022430 11712145 0.05914554729986901 0.375591366364649 chr4 191154276 8986357 0.04701101742552701 0.3244844375550014 chr5 180915260 4184857 0.023131586578158194 0.23377478200151092 chr6 171115067 29937786 0.17495704221066635 1.1478291805488046 chr7 159138663 9462671 0.059461797790773194 0.5786323212557047 chr8 146364022 18412019 0.12579607166028822 0.775312449111346 chr9 141213431 2958470 0.020950344305422336 0.4447506067435458 chr10 135534747 3637403 0.0268374205177068 0.45906559639015604 chr11 135006516 6791943 0.05030826067684022 0.5184884151537466 chr12 133851895 1490154 0.011132856953575443 0.1688026141354629 chr13 115169878 7575729 0.06577873599900835 0.3914227991862508 chr14 107349540 5676403 0.05287775802299665 0.35947808904287304 chr15 102531392 4613635 0.044997292146389666 0.31386584292152436 chr16 90354753 757681 0.008385624163014424 0.2400943770434948 chr17 81195210 2937023 0.03617236780347018 0.5160117721191764 chr18 78077248 6036449 0.0773138033758567 0.9999922328086394 chr19 59128983 1565831 0.02648161562325535 0.7711817998860426 chr20 63025520 4747385 0.07532480493615919 0.40916477967189946 chr21 48129895 760235 0.015795484282689586 0.19271436515380097 chr22 51304566 822483 0.016031380130961444 0.17908445576301718 chrMT 16571 152879 9.225695492124796 5.937604997145742 chrX 155270560 6694880 0.04311751049265231 0.3680423696323684 chrY 59373566 267380 0.004503350868297181 0.11970793547178858