BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819092.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 = 1,495,412 number of mapped reads = 1,357,112 (90.75%) number of supplementary alignments = 5,688 (0.38%) number of secondary alignments = 0 number of mapped bases = 78,438,254 bp number of sequenced bases = 78,413,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,511 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6104 >>>>>>> ACTG content number of A's = 19,249,672 bp (24.55%) number of C's = 13,972,659 bp (17.82%) number of T's = 25,913,570 bp (33.05%) number of G's = 19,276,343 bp (24.58%) number of N's = 1,084 bp (0%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 403,071 number of insertions = 5,798 mapped reads with insertion percentage = 0.43% number of deletions = 15,118 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.22% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.246X There is a 2.3% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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 7696049 0.030876749550806534 0.44805965885242255 chr2 243199373 6214697 0.02555391867724922 0.2784263868523218 chr3 198022430 4269511 0.02156074440658061 0.16112195386159622 chr4 191154276 4449098 0.02327490701803605 0.18232170424238014 chr5 180915260 4306501 0.023803967669725593 0.16730431190166986 chr6 171115067 3388880 0.019804684995974084 0.1870177085551081 chr7 159138663 3918596 0.024623783599338145 0.31559431546525507 chr8 146364022 7175822 0.04902722610342042 0.2765484987528988 chr9 141213431 3301500 0.02337950417761608 0.20659333408831 chr10 135534747 4111393 0.03033460489655837 0.25454800010479206 chr11 135006516 2714236 0.020104481475545964 0.22091361060800865 chr12 133851895 3638705 0.027184560965685244 0.17901753435527115 chr13 115169878 1763227 0.01530979306933016 0.13348607358585515 chr14 107349540 1889557 0.01760191054381789 0.14572865962894907 chr15 102531392 2065991 0.020149838597724293 0.1573163376968412 chr16 90354753 2471523 0.02735354718970899 0.1895172487740508 chr17 81195210 2754074 0.03391916838444041 0.20752957730475763 chr18 78077248 1842921 0.023603816056631505 0.3759350932859556 chr19 59128983 1621268 0.027419176142434245 0.31842365319686444 chr20 63025520 2213567 0.03512175702794677 0.20236699800059196 chr21 48129895 1067526 0.022180102408284913 0.1708835456645354 chr22 51304566 649081 0.012651525012413125 0.12085087325384361 chrMT 16571 4206 0.25381690905799287 0.5735108851725365 chrX 155270560 4664472 0.03004092984529714 0.20829939749581622 chrY 59373566 245853 0.0041407821116892325 0.11634168154905296