BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081691.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 = 2,051,883 number of mapped reads = 1,804,664 (87.95%) number of supplementary alignments = 16,320 (0.8%) number of secondary alignments = 0 number of mapped bases = 120,820,137 bp number of sequenced bases = 120,775,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,550 duplication rate = 4.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2529 >>>>>>> ACTG content number of A's = 33,812,236 bp (28%) number of C's = 21,346,512 bp (17.67%) number of T's = 39,316,463 bp (32.55%) number of G's = 26,217,027 bp (21.71%) number of N's = 82,971 bp (0.07%) GC percentage = 39.38% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,073,164 number of insertions = 10,612 mapped reads with insertion percentage = 0.58% number of deletions = 27,523 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.22% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.3525X There is a 3.18% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9353568 0.03752675906071263 0.5146027059025352 chr2 243199373 10483296 0.043105769026797615 0.3974268409932746 chr3 198022430 8555158 0.043202974531723504 0.24550957276279567 chr4 191154276 8268139 0.043253748610886426 0.264538647262249 chr5 180915260 7571598 0.04185162710984137 0.24229134887025935 chr6 171115067 7348045 0.04294212735807771 0.2903647129617052 chr7 159138663 6774241 0.042568165851688725 0.48312620995285227 chr8 146364022 6294942 0.043008807178037234 0.6085221936776131 chr9 141213431 5184769 0.03671583477070251 0.3459869316840212 chr10 135534747 5529774 0.040799677738727766 0.337586605325274 chr11 135006516 5346733 0.039603518099822675 0.30667591818725437 chr12 133851895 5289566 0.03951805090245454 0.2389280864161457 chr13 115169878 3987846 0.034625772547922644 0.21909064964582298 chr14 107349540 3772548 0.0351426564100787 0.23416065966299313 chr15 102531392 3344798 0.03262218462809907 0.21317685212601964 chr16 90354753 3057995 0.033844318073671234 0.23326769821906612 chr17 81195210 2709772 0.03337354506503524 0.2416890720452279 chr18 78077248 3322185 0.042549975634387116 0.6161053800994335 chr19 59128983 1875404 0.031717169902956054 0.39200568020110593 chr20 63025520 2354843 0.03736332520540886 0.23986667537303702 chr21 48129895 1608801 0.03342623124359611 0.23463720426574214 chr22 51304566 1083395 0.021116931385795176 0.168952646746314 chrMT 16571 17040 1.0283024560980025 1.2445983939410452 chrX 155270560 7361322 0.04740964417208259 0.28297630772762655 chrY 59373566 324359 0.005463020361620186 0.13415906262162663