BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085017.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 = 2,262,130 number of mapped reads = 2,034,969 (89.96%) number of supplementary alignments = 15,693 (0.69%) number of secondary alignments = 0 number of mapped bases = 135,555,563 bp number of sequenced bases = 135,509,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,200 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6549 >>>>>>> ACTG content number of A's = 38,237,749 bp (28.22%) number of C's = 25,723,643 bp (18.98%) number of T's = 41,973,829 bp (30.97%) number of G's = 29,559,210 bp (21.81%) number of N's = 14,976 bp (0.01%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,165,984 number of insertions = 9,391 mapped reads with insertion percentage = 0.46% number of deletions = 27,092 mapped reads with deletion percentage = 1.32% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.3239X There is a 3.77% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10291785 0.041290910163870764 0.447274781247156 chr2 243199373 12700304 0.05222177937111705 0.380021404122483 chr3 198022430 8620600 0.04353345224578852 0.2385352862634484 chr4 191154276 8411821 0.044005403258674684 0.23891373396457372 chr5 180915260 7037777 0.03890095838239405 0.2220369327732644 chr6 171115067 9647388 0.05637953553207562 0.32523922757431006 chr7 159138663 12316163 0.07739265096125635 0.39337755389757867 chr8 146364022 8019616 0.054792263087714274 0.6010524983060124 chr9 141213431 3744908 0.02651948878715368 0.25395269629818523 chr10 135534747 10786995 0.07958840990052536 0.44555747481874364 chr11 135006516 5575209 0.041295851231358344 0.3016485348196672 chr12 133851895 5974692 0.04463658882080078 0.24115159147314505 chr13 115169878 2568660 0.02230322758525454 0.16677327160767833 chr14 107349540 4570109 0.04257222713762909 0.2365269508062341 chr15 102531392 2355407 0.022972544837780023 0.17748191366777133 chr16 90354753 3465977 0.038359653310103124 0.2293630407901179 chr17 81195210 2268437 0.027938064326701047 0.21260980786270028 chr18 78077248 3116751 0.039918812199938196 0.39816999494888683 chr19 59128983 1960999 0.033164767944681206 0.32045670822640043 chr20 63025520 3108204 0.04931659429386699 0.25303826859327766 chr21 48129895 1497581 0.031115401352942905 0.20392488434164682 chr22 51304566 744206 0.014505648483606703 0.1323349658322222 chrMT 16571 17003 1.026069639732062 1.373556265103054 chrX 155270560 6496936 0.041842677710442984 0.24797447680000895 chrY 59373566 258035 0.0043459575933168645 0.08548462290106572