BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124920.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 7,792,336 number of mapped reads = 7,425,459 (95.29%) number of supplementary alignments = 8,131 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,760,696 number of mapped paired reads (second in pair) = 3,664,763 number of mapped paired reads (both in pair) = 7,305,456 number of mapped paired reads (singletons) = 120,003 number of mapped bases = 460,485,327 bp number of sequenced bases = 460,276,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 699,529 duplication rate = 7.07% >>>>>>> Insert size mean insert size = 26,339.8005 std insert size = 1,522,414.6598 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.029 >>>>>>> ACTG content number of A's = 123,511,856 bp (26.83%) number of C's = 84,213,038 bp (18.3%) number of T's = 135,262,303 bp (29.39%) number of G's = 117,285,883 bp (25.48%) number of N's = 3,425 bp (0%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 3,083,635 number of insertions = 50,627 mapped reads with insertion percentage = 0.67% number of deletions = 139,081 mapped reads with deletion percentage = 1.85% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.1488X std coverageData = 0.9455X There is a 10.2% of reference with a coverageData >= 1X There is a 2.76% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 31493172 0.1263514284283368 0.9659801014827462 chr2 243199373 43154012 0.1774429410227139 1.484362085761041 chr3 198022430 28867669 0.14577979373346747 0.5108316326035485 chr4 191154276 30201326 0.15799450910530508 0.6652902227577393 chr5 180915260 30061537 0.16616363373659027 0.5786469660051081 chr6 171115067 23856941 0.1394204579308028 0.7583907760277059 chr7 159138663 29801411 0.18726694342027997 1.2822783290855035 chr8 146364022 30396556 0.2076777857334366 0.713750349315951 chr9 141213431 13265896 0.09394216899949127 0.7450588499032252 chr10 135534747 28573055 0.21081719361604004 1.776311452307767 chr11 135006516 23802220 0.1763042311231852 0.7795529158613375 chr12 133851895 17102850 0.12777443307769382 0.4917663195808109 chr13 115169878 14643749 0.12714912314138252 0.4809392206964557 chr14 107349540 9707113 0.09042528733704867 0.4775266710956267 chr15 102531392 14777642 0.14412797594711285 0.5273335636434516 chr16 90354753 15815917 0.17504244630052831 1.4553374017407856 chr17 81195210 17678693 0.2177307380570849 1.3056837584951535 chr18 78077248 8526828 0.1092101504397286 1.1372662582308584 chr19 59128983 7349512 0.1242962693946554 0.8265073661862161 chr20 63025520 10118091 0.16053958777333371 0.6463818121874421 chr21 48129895 4077896 0.08472688336427911 0.49262396410951254 chr22 51304566 6680400 0.13021063271444494 0.5194574668792216 chrMT 16571 471681 28.464244764950816 20.80777929013718 chrX 155270560 19001017 0.12237359741602014 0.5872568647314526 chrY 59373566 1060143 0.01785547123782324 1.0519188766197214