BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080952.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 = 3,342,098 number of mapped reads = 2,974,027 (88.99%) number of supplementary alignments = 25,581 (0.77%) number of secondary alignments = 0 number of mapped bases = 199,238,332 bp number of sequenced bases = 199,164,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,166 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0281 >>>>>>> ACTG content number of A's = 56,099,294 bp (28.17%) number of C's = 34,359,138 bp (17.25%) number of T's = 64,487,083 bp (32.38%) number of G's = 43,297,298 bp (21.74%) number of N's = 922,127 bp (0.46%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 2,204,385 number of insertions = 15,724 mapped reads with insertion percentage = 0.53% number of deletions = 44,462 mapped reads with deletion percentage = 1.48% homopolymer indels = 49.09% >>>>>>> Coverage mean coverageData = 0.0644X std coverageData = 0.502X There is a 5.1% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% 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% 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 16477269 0.06610723349010232 0.7423024028884743 chr2 243199373 13573133 0.05581072365675877 0.4594413607553492 chr3 198022430 17454355 0.08814332295588939 0.3621216849375138 chr4 191154276 13067630 0.06836169335809156 0.33318762526976875 chr5 180915260 11704002 0.06469328236877309 0.3106527827303338 chr6 171115067 17236710 0.10073169068156926 0.55443453954475 chr7 159138663 10098903 0.06345977030107385 0.5273319932009539 chr8 146364022 14539541 0.09933821714738066 0.9971700382768119 chr9 141213431 10268083 0.07271321805076743 0.6006005823299658 chr10 135534747 9061726 0.06685906161023047 0.4304730989212998 chr11 135006516 8917256 0.06605056010778028 0.38359397420623426 chr12 133851895 9929147 0.0741801003265587 0.3457256262054063 chr13 115169878 5578242 0.048434904133526996 0.2642200636631522 chr14 107349540 5476532 0.05101588698004668 0.3566445291434461 chr15 102531392 4934635 0.048128040629741964 0.26645965997101084 chr16 90354753 4389516 0.0485809086324435 0.33240509735232715 chr17 81195210 3964954 0.048832363386953494 0.27759667835952345 chr18 78077248 5126622 0.06566089522007743 1.019683130665772 chr19 59128983 3378665 0.05714059042754042 0.5453796708317951 chr20 63025520 3090446 0.04903483541270266 0.2890245042600118 chr21 48129895 2750033 0.05713773113363326 0.37854832979788067 chr22 51304566 1534762 0.029914725328735847 0.2052155670735159 chrMT 16571 46086 2.7811236497495626 2.1927661697664784 chrX 155270560 6195662 0.039902361400641566 0.2726780862849584 chrY 59373566 444422 0.0074851828842485224 0.16115598720482197