BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080676.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 = 1,122,822 number of mapped reads = 1,043,514 (92.94%) number of supplementary alignments = 8,838 (0.79%) number of secondary alignments = 0 number of mapped bases = 70,494,407 bp number of sequenced bases = 70,467,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,058 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2372 >>>>>>> ACTG content number of A's = 19,696,122 bp (27.95%) number of C's = 12,878,244 bp (18.28%) number of T's = 22,458,879 bp (31.87%) number of G's = 15,431,057 bp (21.9%) number of N's = 3,303 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 486,980 number of insertions = 5,490 mapped reads with insertion percentage = 0.52% number of deletions = 16,534 mapped reads with deletion percentage = 1.57% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.1945X There is a 2.07% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 8724233 0.035001850607224765 0.2626799065999207 chr2 243199373 4804639 0.01975596787414415 0.23148680044665293 chr3 198022430 4551676 0.022985658745829956 0.1628767865946436 chr4 191154276 3083980 0.016133460702704865 0.13785945041660824 chr5 180915260 3305758 0.018272411072454583 0.14483812318951517 chr6 171115067 4286541 0.025050634494974074 0.1993662235565812 chr7 159138663 4524094 0.028428628937268375 0.32983713847274043 chr8 146364022 7491368 0.05118312477092219 0.2764399924153405 chr9 141213431 2241478 0.015872980240810096 0.15449148876511215 chr10 135534747 3391383 0.0250222402377746 0.1811427688313761 chr11 135006516 2961968 0.02193944475983663 0.1686020245834599 chr12 133851895 2355464 0.017597539429680842 0.14323713911576688 chr13 115169878 1486497 0.012906994657057812 0.12211030153276645 chr14 107349540 1422630 0.01325231575282018 0.12497964715214707 chr15 102531392 1271028 0.012396476583483817 0.12324719883844024 chr16 90354753 1718546 0.019019984482720017 0.15176655195191385 chr17 81195210 1086646 0.013383129374257422 0.12618576842684165 chr18 78077248 2322369 0.029744503802183193 0.2228112228821069 chr19 59128983 1056270 0.017863828302272677 0.17408939946440477 chr20 63025520 1823223 0.028928329349761812 0.18479407840671555 chr21 48129895 1067312 0.02217565610729049 0.16254759361147683 chr22 51304566 656594 0.012797964220182664 0.12130118701242162 chrMT 16571 9022 0.5444451149598697 0.7570008447625526 chrX 155270560 4707491 0.03031798816208301 0.19298900119339704 chrY 59373566 144197 0.0024286397081152242 0.057383516325162504