BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084848.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 = 2,493,198 number of mapped reads = 2,233,055 (89.57%) number of supplementary alignments = 18,786 (0.75%) number of secondary alignments = 0 number of mapped bases = 155,237,941 bp number of sequenced bases = 155,176,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,497 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2579 >>>>>>> ACTG content number of A's = 45,422,575 bp (29.27%) number of C's = 28,395,213 bp (18.3%) number of T's = 49,913,241 bp (32.17%) number of G's = 31,420,891 bp (20.25%) number of N's = 25,071 bp (0.02%) GC percentage = 38.55% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,257,796 number of insertions = 12,423 mapped reads with insertion percentage = 0.55% number of deletions = 34,289 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.4195X There is a 4.02% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.14% 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% 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 14017167 0.0562372400267761 0.5627640791633329 chr2 243199373 13045243 0.053640117731718 0.38275629722910004 chr3 198022430 10174711 0.05138160863898095 0.27019465596835307 chr4 191154276 10484904 0.05485048108471296 0.28701284799056537 chr5 180915260 12485978 0.06901561537705553 0.3160366041071741 chr6 171115067 9012399 0.052668646648164535 0.27729327839507123 chr7 159138663 8756104 0.05502185223210025 0.3325893727892081 chr8 146364022 7801734 0.05330363222732428 1.142197982016245 chr9 141213431 6089468 0.04312244208555488 0.35835399768682474 chr10 135534747 7033533 0.051894684984360506 0.3562035904459223 chr11 135006516 6792813 0.05031470481024782 0.32473644264359514 chr12 133851895 6659011 0.049749097687410405 0.26870129005636684 chr13 115169878 5465081 0.047452346871462346 0.25980527710577767 chr14 107349540 3538856 0.0329657304539917 0.2286643583537354 chr15 102531392 4195639 0.04092053095309581 0.23994537326902338 chr16 90354753 3677990 0.040706104304219615 0.25876689451933627 chr17 81195210 3388362 0.041731057780378916 0.2556963272827727 chr18 78077248 4493444 0.05755126000342635 0.6455755332484061 chr19 59128983 2335371 0.039496214572132926 0.42228041033877717 chr20 63025520 2836536 0.04500614988975894 0.2587911998793184 chr21 48129895 2281700 0.047407126069982077 0.2731643192177408 chr22 51304566 1249996 0.02436422520365926 0.18141950553571692 chrMT 16571 162349 9.797175789029026 5.5460139201256675 chrX 155270560 8915874 0.057421535672956936 0.30473432583552973 chrY 59373566 343678 0.0057884008516517265 0.1300974397171524