BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084271.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 = 1,508,527 number of mapped reads = 1,213,716 (80.46%) number of supplementary alignments = 7,540 (0.5%) number of secondary alignments = 0 number of mapped bases = 79,438,159 bp number of sequenced bases = 79,412,258 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,432 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9261 >>>>>>> ACTG content number of A's = 23,781,868 bp (29.95%) number of C's = 14,615,724 bp (18.4%) number of T's = 24,023,303 bp (30.25%) number of G's = 16,990,464 bp (21.4%) number of N's = 899 bp (0%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 681,900 number of insertions = 5,784 mapped reads with insertion percentage = 0.47% number of deletions = 16,574 mapped reads with deletion percentage = 1.35% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2077X There is a 2.35% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 6408781 0.025712196721066543 0.2922109820205696 chr2 243199373 7090290 0.029154228123770696 0.236508937337879 chr3 198022430 5327722 0.026904639035083045 0.17568702339609593 chr4 191154276 5361592 0.02804850674645646 0.1811874687928678 chr5 180915260 4942449 0.027319138252903597 0.1767910750937822 chr6 171115067 4740950 0.027706210114156693 0.20126137082240741 chr7 159138663 4398602 0.027640058783200912 0.23397605081225725 chr8 146364022 4116453 0.028124760058862008 0.23537248345770123 chr9 141213431 3167943 0.022433723035877515 0.18879241482324743 chr10 135534747 3604779 0.02659671471552605 0.21236104799406105 chr11 135006516 3461173 0.02563708110207066 0.18583784188781052 chr12 133851895 3694064 0.027598144949684874 0.17792333709274213 chr13 115169878 2679188 0.023262922966715307 0.16261632261394895 chr14 107349540 2354691 0.021934802887837248 0.1635579631333181 chr15 102531392 2357248 0.022990500314284235 0.16275879915265978 chr16 90354753 2055862 0.022753224725211744 0.17250793872464282 chr17 81195210 2007700 0.024726828097371752 0.1844779381167008 chr18 78077248 2078416 0.02661999562279654 0.350027373337241 chr19 59128983 1346098 0.022765451589113243 0.2233982648789203 chr20 63025520 1591075 0.025244932528918445 0.17310701922655433 chr21 48129895 1134654 0.023574828077227262 0.1680436047268713 chr22 51304566 810418 0.01579621587677011 0.13353821219586423 chrMT 16571 9168 0.5532556876470943 0.8587303942611129 chrX 155270560 4532147 0.029188707762759405 0.19149427042754336 chrY 59373566 166696 0.0028075793864225707 0.06609210478905883