BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818922.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,676,464 number of mapped reads = 1,643,543 (98.04%) number of supplementary alignments = 26,534 (1.58%) number of secondary alignments = 0 number of mapped bases = 152,007,335 bp number of sequenced bases = 151,907,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 458,030 duplication rate = 23.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2442 >>>>>>> ACTG content number of A's = 43,774,987 bp (28.82%) number of C's = 31,753,252 bp (20.9%) number of T's = 44,096,198 bp (29.03%) number of G's = 32,280,775 bp (21.25%) number of N's = 2,335 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 926,963 number of insertions = 23,890 mapped reads with insertion percentage = 1.41% number of deletions = 51,605 mapped reads with deletion percentage = 3.06% homopolymer indels = 40.43% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.6196X There is a 3.16% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 14516448 0.05824036843623351 0.8435752625366442 chr2 243199373 11851738 0.04873260096768424 1.07028818212972 chr3 198022430 8891266 0.04490029740570298 0.3030539777980267 chr4 191154276 7764444 0.040618730391362004 0.37185652308873546 chr5 180915260 6736263 0.037234354912902314 0.30028327754797635 chr6 171115067 7739690 0.045230908859709006 0.3323061729268249 chr7 159138663 13694114 0.08605145815508077 1.2428438614673138 chr8 146364022 13170386 0.08998376663904467 0.5229144962317693 chr9 141213431 5736675 0.04062414573016075 0.47578304807737526 chr10 135534747 7016119 0.05176620132695566 0.7270596625806792 chr11 135006516 6627511 0.04909030464870303 0.3687871727893597 chr12 133851895 5915432 0.04419386068460219 0.3091144777795762 chr13 115169878 4578641 0.03975554267757408 0.2822287717902122 chr14 107349540 4531848 0.04221581201000023 0.3300795023686647 chr15 102531392 4324507 0.04217739480216947 0.2995882987775655 chr16 90354753 3713685 0.041101158231266484 0.7513736373275461 chr17 81195210 3589606 0.04420957837291141 0.37976101423474184 chr18 78077248 2998339 0.038402211614835605 0.5191654090164897 chr19 59128983 2495451 0.042203516336480874 0.6595099226015463 chr20 63025520 6085137 0.09655036562966875 0.48723992611513095 chr21 48129895 1506886 0.031308732337770526 0.2917346404374845 chr22 51304566 1351537 0.026343405770160887 0.25896897659007667 chrMT 16571 279838 16.88721260032587 10.443480419016337 chrX 155270560 6347527 0.040880428331037125 0.34206576118609655 chrY 59373566 544247 0.00916648664828385 0.8642886593865243