BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818837.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 = 1,576,195 number of mapped reads = 1,522,700 (96.61%) number of supplementary alignments = 26,413 (1.68%) number of secondary alignments = 0 number of mapped bases = 140,847,026 bp number of sequenced bases = 140,761,731 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,733 duplication rate = 21.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2973 >>>>>>> ACTG content number of A's = 41,557,499 bp (29.52%) number of C's = 29,032,187 bp (20.63%) number of T's = 40,352,962 bp (28.67%) number of G's = 29,816,773 bp (21.18%) number of N's = 2,310 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 832,767 number of insertions = 24,111 mapped reads with insertion percentage = 1.54% number of deletions = 45,581 mapped reads with deletion percentage = 2.93% homopolymer indels = 39.03% >>>>>>> Coverage mean coverageData = 0.0455X std coverageData = 0.4927X There is a 3.06% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 12503845 0.05016575264620905 0.6735742313386879 chr2 243199373 10696510 0.043982473589683144 0.7181414760408259 chr3 198022430 8669377 0.04377977282674493 0.29164406278133204 chr4 191154276 7262754 0.037994201081852856 0.3209265926286763 chr5 180915260 6441905 0.03560730587347911 0.27388660061857273 chr6 171115067 7035826 0.04111751304752141 0.30100952329404135 chr7 159138663 12853367 0.08076834854393618 0.9573356427990435 chr8 146364022 12739307 0.0870385141506975 0.5011829140942617 chr9 141213431 5254586 0.03721024241667211 0.43243404130640667 chr10 135534747 6496121 0.04792956156106596 0.6489472671331824 chr11 135006516 6330039 0.04688691470269479 0.34729528610039734 chr12 133851895 5604458 0.041870591372651096 0.2877613480539543 chr13 115169878 4468578 0.03879988481015843 0.2723771181419718 chr14 107349540 4232304 0.03942545072852664 0.30813689944173606 chr15 102531392 3906608 0.038101579660597996 0.2696979691157464 chr16 90354753 3493753 0.03866706381234864 0.513508892525429 chr17 81195210 3468547 0.042718616036586395 0.34764735489335896 chr18 78077248 2783998 0.03565696885218086 0.486840209415304 chr19 59128983 1654424 0.02797991638043225 0.5747534428928123 chr20 63025520 5691841 0.09031009978180267 0.4414820471751809 chr21 48129895 1410072 0.029297217457050342 0.27358035086692384 chr22 51304566 1288624 0.025117140645922235 0.24117807444004055 chrMT 16571 192990 11.646249471969103 7.965631442819388 chrX 155270560 5894526 0.037962933862027676 0.3065186565334289 chrY 59373566 472666 0.007960882794205084 0.5583011416101963