BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081950.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 = 2,864,894 number of mapped reads = 2,648,374 (92.44%) number of supplementary alignments = 15,794 (0.55%) number of secondary alignments = 0 number of mapped bases = 180,887,942 bp number of sequenced bases = 180,818,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,456 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2923 >>>>>>> ACTG content number of A's = 51,279,634 bp (28.36%) number of C's = 33,403,388 bp (18.47%) number of T's = 57,181,030 bp (31.62%) number of G's = 38,931,280 bp (21.53%) number of N's = 23,500 bp (0.01%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,362,558 number of insertions = 12,808 mapped reads with insertion percentage = 0.48% number of deletions = 39,033 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.4586X There is a 4.93% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17454884 0.07002945039803933 0.7556622173773154 chr2 243199373 15388801 0.06327648303599862 0.6175867947379979 chr3 198022430 11036469 0.055733428783799895 0.2758531742158329 chr4 191154276 9790504 0.051217813197126705 0.2788569329175588 chr5 180915260 9139483 0.050518032586084775 0.2597584601701006 chr6 171115067 15660798 0.09152202827352428 0.42456939610869254 chr7 159138663 11125955 0.06991358850363096 0.4769808832244866 chr8 146364022 10362894 0.07080219481806806 0.6737453266701292 chr9 141213431 10682403 0.07564721658805953 0.5350902669434521 chr10 135534747 7687991 0.056723395071523616 0.518793683317961 chr11 135006516 8654875 0.06410709094959535 0.3792862394613194 chr12 133851895 7681376 0.057387129259544666 0.2829766659015318 chr13 115169878 5239047 0.045489733001193244 0.2406541495250714 chr14 107349540 3930444 0.03661351506489921 0.26392482186022015 chr15 102531392 3776811 0.03683565517183264 0.22020524146348736 chr16 90354753 3449190 0.03817386341590685 0.27204585038112566 chr17 81195210 6125439 0.0754408911560177 0.36930404668624695 chr18 78077248 4227545 0.054145671220379075 0.7715908678419444 chr19 59128983 2456049 0.04153714262259508 0.5844374357497908 chr20 63025520 4133276 0.06558099004974492 0.29961430641695225 chr21 48129895 1945305 0.04041781100914515 0.2674682615926765 chr22 51304566 1485982 0.028963932761852034 0.18975790927018488 chrMT 16571 41042 2.476736467322431 2.0906015166713083 chrX 155270560 9021988 0.05810494919320185 0.32420107528267167 chrY 59373566 389391 0.006558322604372458 0.1659631001465522