BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083782.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 = 3,339,859 number of mapped reads = 1,277,361 (38.25%) number of supplementary alignments = 6,264 (0.19%) number of secondary alignments = 0 number of mapped bases = 76,406,840 bp number of sequenced bases = 76,381,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,626 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6819 >>>>>>> ACTG content number of A's = 21,758,209 bp (28.49%) number of C's = 14,903,663 bp (19.51%) number of T's = 22,781,571 bp (29.83%) number of G's = 16,937,722 bp (22.18%) number of N's = 821 bp (0%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 649,649 number of insertions = 5,575 mapped reads with insertion percentage = 0.43% number of deletions = 15,595 mapped reads with deletion percentage = 1.21% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.213X There is a 2.26% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5907182 0.023699768435080447 0.2677967207785327 chr2 243199373 6837124 0.028113246821569723 0.2617957169311654 chr3 198022430 4871132 0.02459889013582956 0.16731844345825678 chr4 191154276 4324372 0.02262241834443714 0.169306028788424 chr5 180915260 4785591 0.02645211354752496 0.17393346696775405 chr6 171115067 3989290 0.02331349348681259 0.1773689274974861 chr7 159138663 4267811 0.026818190624109995 0.2640612867939852 chr8 146364022 3682769 0.025161709480762972 0.22075781616177367 chr9 141213431 3384975 0.023970630668976523 0.22106122742251835 chr10 135534747 3771359 0.02782577223536633 0.22797438744601312 chr11 135006516 3794833 0.0281085173696357 0.21436200658102766 chr12 133851895 3749773 0.028014343764053547 0.17985010063979093 chr13 115169878 2572296 0.022334798340239624 0.15990883303819747 chr14 107349540 2442475 0.022752542768231705 0.16612369883131523 chr15 102531392 2186406 0.021324259403403007 0.15776624811985437 chr16 90354753 2051831 0.02270861168753347 0.1735603260308566 chr17 81195210 1853763 0.02283094039660714 0.1778168371564217 chr18 78077248 2038456 0.02610819479702973 0.40846378734234323 chr19 59128983 1439694 0.024348363982515987 0.2446724176469906 chr20 63025520 1661801 0.026367112877450277 0.1768399958413481 chr21 48129895 1085391 0.022551285432889475 0.1674185806926692 chr22 51304566 904760 0.017635077548458358 0.14033325580926864 chrMT 16571 11599 0.699957757528212 0.90173094632562 chrX 155270560 4573750 0.029456646514316686 0.19785758661791206 chrY 59373566 218407 0.003678522526337731 0.08943152035626588