BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080646.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 = 1,537,829 number of mapped reads = 1,362,337 (88.59%) number of supplementary alignments = 13,200 (0.86%) number of secondary alignments = 0 number of mapped bases = 89,412,458 bp number of sequenced bases = 89,379,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,785 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1876 >>>>>>> ACTG content number of A's = 23,984,431 bp (26.83%) number of C's = 16,564,714 bp (18.53%) number of T's = 28,195,400 bp (31.55%) number of G's = 20,631,192 bp (23.08%) number of N's = 3,724 bp (0%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 615,799 number of insertions = 6,530 mapped reads with insertion percentage = 0.48% number of deletions = 20,534 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2407X There is a 2.49% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 10737932 0.04308086357786848 0.276981285132124 chr2 243199373 6033104 0.024807235008784335 0.36775510756043334 chr3 198022430 5509830 0.027824272230171098 0.18721318920193167 chr4 191154276 3751094 0.019623385249305122 0.1619948002169547 chr5 180915260 4117214 0.02275769329795618 0.1702531815601867 chr6 171115067 5196040 0.030365765511461362 0.2278128200541178 chr7 159138663 6687935 0.04202583378496777 0.45706022997920775 chr8 146364022 10321371 0.07051849805001942 0.3209931996980953 chr9 141213431 2830810 0.020046322647595753 0.17839246888897736 chr10 135534747 4166424 0.03074063361773937 0.20554724785978878 chr11 135006516 3753074 0.027799206373120538 0.20029304060815561 chr12 133851895 2876349 0.02148904204904981 0.16609324609065437 chr13 115169878 1774116 0.015404340360593245 0.1412972657416097 chr14 107349540 1762427 0.01641764836626221 0.145145417703917 chr15 102531392 1668579 0.01627383543178659 0.15324793451107757 chr16 90354753 2234884 0.02473454827550688 0.1793205863394022 chr17 81195210 1518757 0.018705007352034682 0.15493733932865975 chr18 78077248 2698093 0.03455671234723847 0.25804774379054635 chr19 59128983 1472799 0.024908241699337193 0.2006227322933082 chr20 63025520 2363752 0.03750468064365038 0.22148051691767015 chr21 48129895 1296153 0.026930310153388034 0.18886798314139533 chr22 51304566 889976 0.01734691606201288 0.14806768049279662 chrMT 16571 8629 0.5207289843702855 0.7617568644893211 chrX 155270560 5572629 0.03588979778265758 0.22033516862633182 chrY 59373566 170487 0.0028714293495526277 0.0659468864388906