BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038404.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 17,668,008 number of mapped reads = 16,394,642 (92.79%) number of supplementary alignments = 219,096 (1.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,320,732 number of mapped paired reads (second in pair) = 8,073,910 number of mapped paired reads (both in pair) = 16,090,192 number of mapped paired reads (singletons) = 304,450 number of mapped bases = 2,209,045,635 bp number of sequenced bases = 2,207,602,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,257,605 duplication rate = 14.21% >>>>>>> Insert size mean insert size = 74,022.0374 std insert size = 2,646,990.012 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 53.3809 >>>>>>> ACTG content number of A's = 632,401,450 bp (28.65%) number of C's = 436,067,141 bp (19.75%) number of T's = 644,041,642 bp (29.17%) number of G's = 494,917,493 bp (22.42%) number of N's = 174,500 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 27,723,992 number of insertions = 370,222 mapped reads with insertion percentage = 2.16% number of deletions = 762,638 mapped reads with deletion percentage = 4.5% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.7136X std coverageData = 8.8507X There is a 26.4% of reference with a coverageData >= 1X There is a 15.42% of reference with a coverageData >= 2X There is a 8.97% of reference with a coverageData >= 3X There is a 5.66% of reference with a coverageData >= 4X There is a 3.58% of reference with a coverageData >= 5X There is a 2.35% of reference with a coverageData >= 6X There is a 1.56% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.73% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189661642 0.7609274602368995 12.504623009093237 chr2 243199373 197987089 0.8140937476841275 10.789813962136998 chr3 198022430 163647177 0.8264072761858341 1.8652427717022504 chr4 191154276 94672978 0.4952699985638825 7.799068843543446 chr5 180915260 152202073 0.8412893030692933 1.8179932473274223 chr6 171115067 130832940 0.7645904144723854 7.9996722649419345 chr7 159138663 106462277 0.6689906462265552 9.209922225025217 chr8 146364022 141995562 0.9701534575211387 3.7687300620807016 chr9 141213431 94007131 0.6657095598789041 16.114608652161294 chr10 135534747 131322049 0.9689179483988707 20.226323627571706 chr11 135006516 100480308 0.7442626547003109 7.696549572461761 chr12 133851895 91668812 0.6848525528906408 1.799146201924309 chr13 115169878 74524226 0.6470808799502245 1.5405895178791342 chr14 107349540 71423970 0.6653402520402044 1.667051733099472 chr15 102531392 59096512 0.5763748140667007 1.4954199170893416 chr16 90354753 66219345 0.7328817002023126 8.395839398082497 chr17 81195210 52364032 0.6449152850272818 10.934551873314682 chr18 78077248 88486041 1.133314035351246 11.338434798096248 chr19 59128983 27474942 0.464661162868301 5.261382835042797 chr20 63025520 58446355 0.9273442726057635 3.1589094012013526 chr21 48129895 20741741 0.43095338146904333 3.8417105469197432 chr22 51304566 11972757 0.23336630505752645 0.9320263839014713 chrMT 16571 3400157 205.18719449640938 117.74655964605685 chrX 155270560 76031838 0.48967323876464414 2.100270209145906 chrY 59373566 3923681 0.06608464446956075 7.757844619678648