BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080963.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 = 6,069,328 number of mapped reads = 5,354,176 (88.22%) number of supplementary alignments = 46,503 (0.77%) number of secondary alignments = 0 number of mapped bases = 359,235,948 bp number of sequenced bases = 359,107,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 457,968 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2339 >>>>>>> ACTG content number of A's = 100,250,809 bp (27.92%) number of C's = 63,127,910 bp (17.58%) number of T's = 117,044,292 bp (32.59%) number of G's = 77,978,172 bp (21.71%) number of N's = 706,515 bp (0.2%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 3,507,830 number of insertions = 27,749 mapped reads with insertion percentage = 0.51% number of deletions = 78,123 mapped reads with deletion percentage = 1.44% homopolymer indels = 49.64% >>>>>>> Coverage mean coverageData = 0.116X std coverageData = 0.73X There is a 7.24% of reference with a coverageData >= 1X There is a 2.52% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 30542744 0.12253828647431936 0.8811547091538754 chr2 243199373 24753452 0.10178254859234362 0.7133213124735575 chr3 198022430 31938475 0.16128715822747958 0.598626663969879 chr4 191154276 22852329 0.11954913841425133 0.5332118028423484 chr5 180915260 20596741 0.11384744990555247 0.4982968241812895 chr6 171115067 30734908 0.17961543970876626 0.8788446873797315 chr7 159138663 18085581 0.1136466818248938 0.6603043436143377 chr8 146364022 27484686 0.18778307417652132 1.2958215162882394 chr9 141213431 18773530 0.13294436561066206 0.9605753816351272 chr10 135534747 15530618 0.11458772265978406 0.6129225352107494 chr11 135006516 15635042 0.11580953618564603 0.6197708467640533 chr12 133851895 14577182 0.10890530911049111 0.5171680594342047 chr13 115169878 10211053 0.08866079549029304 0.43782207145200347 chr14 107349540 10563217 0.09840020739725573 0.5940225010587187 chr15 102531392 9183191 0.08956467693328497 0.44071791711540476 chr16 90354753 8153914 0.09024333230151158 0.5487048607084748 chr17 81195210 7517271 0.09258269053063599 0.4528753445554233 chr18 78077248 9243149 0.11838466693908065 1.61180120154566 chr19 59128983 6338924 0.10720502329627418 0.6990978350674176 chr20 63025520 5822959 0.09239049515180517 0.4742440354040097 chr21 48129895 6618059 0.13750412295725972 0.6888203275667667 chr22 51304566 2767016 0.0539331333589295 0.3377697596997344 chrMT 16571 405452 24.467563816305596 14.37537918703673 chrX 155270560 10205709 0.0657285515039039 0.42115705128027603 chrY 59373566 700746 0.011802322939471078 0.23614578634299152