BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081004.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 = 3,321,411 number of mapped reads = 2,860,023 (86.11%) number of supplementary alignments = 13,657 (0.41%) number of secondary alignments = 0 number of mapped bases = 184,385,284 bp number of sequenced bases = 184,318,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,656 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3218 >>>>>>> ACTG content number of A's = 50,879,917 bp (27.6%) number of C's = 37,122,461 bp (20.14%) number of T's = 54,190,704 bp (29.4%) number of G's = 42,123,272 bp (22.85%) number of N's = 2,455 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,372,918 number of insertions = 12,738 mapped reads with insertion percentage = 0.44% number of deletions = 37,672 mapped reads with deletion percentage = 1.3% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.4273X There is a 4.91% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14650598 0.05877858173922062 0.6212219986542726 chr2 243199373 15517667 0.0638063610468272 0.4793162273913481 chr3 198022430 12059835 0.0609013584976207 0.2878271631611603 chr4 191154276 11376878 0.05951673296599444 0.31568057216386025 chr5 180915260 10876122 0.06011721730936351 0.2884928062565933 chr6 171115067 10339963 0.060426958194160656 0.37474892014543876 chr7 159138663 10445107 0.06563525671948117 0.7755418954270834 chr8 146364022 9163112 0.06260494809304981 0.4048137882986602 chr9 141213431 7867848 0.055716003387808063 0.40043910189236886 chr10 135534747 8359448 0.06167752687065554 0.38906589687277837 chr11 135006516 8833923 0.0654333084189803 0.4221307770438934 chr12 133851895 8302588 0.06202816926872795 0.29691328004771056 chr13 115169878 5556590 0.04824690358706467 0.25586353110592397 chr14 107349540 5791359 0.05394861496379025 0.29305075114030105 chr15 102531392 5603320 0.05464979935120748 0.2891509795765257 chr16 90354753 5343692 0.0591412385356197 0.32198852183109966 chr17 81195210 5122538 0.06308916498891991 0.34283097281248925 chr18 78077248 5000743 0.06404865857976962 0.7672713513952087 chr19 59128983 4016368 0.06792553831003655 0.5006204929732224 chr20 63025520 4141274 0.06570789102573053 0.31152250150353006 chr21 48129895 2474179 0.05140628293496173 0.30156401159169405 chr22 51304566 2260757 0.044065415152327765 0.2455732213740527 chrMT 16571 11873 0.7164926679138254 0.9722772577150728 chrX 155270560 10781667 0.06943793466063367 0.3513124284861982 chrY 59373566 487835 0.008216366859285494 0.17185328583282392