BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081918.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 = 1,870,559 number of mapped reads = 1,723,394 (92.13%) number of supplementary alignments = 13,661 (0.73%) number of secondary alignments = 0 number of mapped bases = 116,573,530 bp number of sequenced bases = 116,528,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,811 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4112 >>>>>>> ACTG content number of A's = 32,448,530 bp (27.85%) number of C's = 22,242,276 bp (19.09%) number of T's = 35,630,377 bp (30.58%) number of G's = 26,205,976 bp (22.49%) number of N's = 1,304 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,008,445 number of insertions = 9,849 mapped reads with insertion percentage = 0.57% number of deletions = 27,017 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3639X There is a 3.34% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9250872 0.037114740027066974 0.6446610262668454 chr2 243199373 9988778 0.04107238385026593 0.4673984453574352 chr3 198022430 7830816 0.039545095977258735 0.21995586736360143 chr4 191154276 7727745 0.04042674410275813 0.2503474930057544 chr5 180915260 7135768 0.039442598706156684 0.2172991248479085 chr6 171115067 6792234 0.03969395634809879 0.2526746398625206 chr7 159138663 6454584 0.04055949621745911 0.5019831351357722 chr8 146364022 5924201 0.04047580080848011 0.39652041611493494 chr9 141213431 4910718 0.03477514826475677 0.3460092594981046 chr10 135534747 5528866 0.04079297834967737 0.3965624263141079 chr11 135006516 5271841 0.03904878931917627 0.3100501723530175 chr12 133851895 5271963 0.03938653987677948 0.2181563129474838 chr13 115169878 3669666 0.0318630710019507 0.1934223694183491 chr14 107349540 3514557 0.03273937643328514 0.2206565820608791 chr15 102531392 3254097 0.03173756774900705 0.1991825040311309 chr16 90354753 3289546 0.036407005617070304 0.24900421150731905 chr17 81195210 3041374 0.037457554454259065 0.23433803173463175 chr18 78077248 3115952 0.03990857874498855 0.663427684884 chr19 59128983 2321813 0.03926691923654428 0.4968011381473234 chr20 63025520 2328497 0.03694530406095817 0.2214383622165304 chr21 48129895 1493328 0.0310270363149556 0.21592415010743174 chr22 51304566 1235973 0.024090896704983333 0.1693104771715409 chrMT 16571 1955 0.11797718906523444 0.338287083270571 chrX 155270560 6880995 0.044316160127199904 0.26155299449222036 chrY 59373566 337391 0.005682511978478773 0.15683689573027876