BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548937.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,024,579 number of mapped reads = 7,027,746 (87.58%) number of secondary alignments = 0 number of mapped bases = 277,618,760 bp number of sequenced bases = 277,588,333 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 283,277 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.7776 >>>>>>> ACTG content number of A's = 81,113,262 bp (29.22%) number of C's = 57,613,565 bp (20.76%) number of T's = 81,442,710 bp (29.34%) number of G's = 57,416,403 bp (20.68%) number of N's = 2,393 bp (0%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 925,734 number of insertions = 10,742 mapped reads with insertion percentage = 0.15% number of deletions = 23,447 mapped reads with deletion percentage = 0.33% homopolymer indels = 38.81% >>>>>>> Coverage mean coverageData = 0.0897X std coverageData = 1.1713X There is a 7.37% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21619011 0.08673603665765792 1.1960533580584334 chr2 243199373 23500053 0.0966287565223287 0.7082636252024722 chr3 198022430 18655412 0.0942085803108264 0.3604017218507872 chr4 191154276 18459988 0.09657114863598447 0.3875919222794308 chr5 180915260 17281095 0.0955203834104431 0.37719487891510983 chr6 171115067 16270130 0.09508297711738031 0.4234519369194314 chr7 159138663 15643063 0.09829831861789615 1.1043252574741067 chr8 146364022 14550661 0.09941419210248267 4.4327340518687315 chr9 141213431 11633409 0.08238174596862533 0.720854339989362 chr10 135534747 12825981 0.0946324192422774 0.5919763453338404 chr11 135006516 12471906 0.0923800300127736 0.7124615904926795 chr12 133851895 12677120 0.09471005248001906 0.3920733708677227 chr13 115169878 8953356 0.07774043139995337 0.3203224388593847 chr14 107349540 8407678 0.0783205778059226 0.4559532178319706 chr15 102531392 7803357 0.07610700340438176 0.32624105099412415 chr16 90354753 7434046 0.08227620300173916 0.4154466540119052 chr17 81195210 7105856 0.08751570443625924 0.39270658432920097 chr18 78077248 7403813 0.09482676694752357 1.3940378061010783 chr19 59128983 5660469 0.09573087025697702 1.1981362269302978 chr20 63025520 5361147 0.08506311411631352 0.366307251870933 chr21 48129895 3455979 0.07180524702993846 0.40802099248976015 chr22 51304566 2906332 0.05664860316721128 0.3248666328678531 chrMT 16571 6340 0.38259610162331786 0.7082411809892604 chrX 155270560 16516790 0.10637425407623957 0.5243644882549091 chrY 59373566 1015768 0.01710808476620724 0.21892395703881581