BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084783.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,085,550 number of mapped reads = 1,888,846 (90.57%) number of supplementary alignments = 19,516 (0.94%) number of secondary alignments = 0 number of mapped bases = 127,576,423 bp number of sequenced bases = 127,528,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,802 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2077 >>>>>>> ACTG content number of A's = 35,859,265 bp (28.12%) number of C's = 23,691,315 bp (18.58%) number of T's = 40,240,763 bp (31.55%) number of G's = 27,694,552 bp (21.72%) number of N's = 42,856 bp (0.03%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,084,723 number of insertions = 10,032 mapped reads with insertion percentage = 0.53% number of deletions = 29,527 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.3534X There is a 3.32% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 9165410 0.03677186425144353 0.5530980032346531 chr2 243199373 11455043 0.04710144955842464 0.4296802672030838 chr3 198022430 8752989 0.044202007823053176 0.2499502823692219 chr4 191154276 6950039 0.03635827115894598 0.24168161283458886 chr5 180915260 9168659 0.050679301458594485 0.26965318137139366 chr6 171115067 8122090 0.04746566238962464 0.309117600766868 chr7 159138663 7246576 0.04553623779030995 0.37483403354112627 chr8 146364022 7200357 0.049194856096534435 0.5749271521919301 chr9 141213431 5557249 0.039353544210677806 0.33488201931134526 chr10 135534747 5998790 0.04426016304143763 0.3186548554266044 chr11 135006516 7185773 0.05322537913651516 0.36864139611559055 chr12 133851895 5663018 0.0423080898481116 0.2500466795801243 chr13 115169878 3971618 0.03448486764916083 0.2229098474372931 chr14 107349540 3492404 0.03253301318291629 0.22978714562441308 chr15 102531392 3450543 0.03365352730215542 0.2211676677702068 chr16 90354753 2842816 0.03146282741761244 0.2296329535517769 chr17 81195210 3517002 0.0433153876934366 0.3042527571465009 chr18 78077248 3513583 0.04500136838839402 0.5754327766024474 chr19 59128983 2102043 0.0355501294517445 0.42149846448981454 chr20 63025520 2294071 0.036399080880252954 0.23624029039108893 chr21 48129895 1710605 0.035541423890494674 0.23584984317521182 chr22 51304566 1113580 0.021705280578730557 0.1728526423165797 chrMT 16571 4630 0.2794037776839056 0.6237103287708224 chrX 155270560 6822199 0.043937492078343764 0.274705463608013 chrY 59373566 275336 0.004637349894058915 0.11266413962175767