BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082497.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 = 1,296,230 number of mapped reads = 1,161,629 (89.62%) number of supplementary alignments = 10,161 (0.78%) number of secondary alignments = 0 number of mapped bases = 79,624,017 bp number of sequenced bases = 79,595,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,865 duplication rate = 2.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5828 >>>>>>> ACTG content number of A's = 23,281,140 bp (29.25%) number of C's = 14,977,493 bp (18.82%) number of T's = 24,129,349 bp (30.31%) number of G's = 17,206,187 bp (21.62%) number of N's = 1,669 bp (0%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 685,304 number of insertions = 6,526 mapped reads with insertion percentage = 0.56% number of deletions = 17,159 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2396X There is a 2.37% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6269048 0.025151584276293538 0.37397815262665535 chr2 243199373 6724254 0.027649142006628446 0.2725763441571838 chr3 198022430 5513705 0.027843840720467878 0.1768889613312616 chr4 191154276 5486651 0.028702737468451922 0.18221390338147558 chr5 180915260 5027604 0.027789828232289527 0.17696378932306525 chr6 171115067 4731512 0.027651054246438742 0.1937032229768447 chr7 159138663 4396898 0.027629351140143737 0.2835730025123874 chr8 146364022 4186769 0.028605178668839805 0.4218058914922925 chr9 141213431 3384091 0.023964370641203384 0.21744496328206475 chr10 135534747 3681358 0.027161728497563802 0.2181416466822234 chr11 135006516 3603361 0.02669027471237018 0.20129187382393077 chr12 133851895 3523053 0.026320531360426388 0.17219972552599 chr13 115169878 2612050 0.022679975401206903 0.15872353637600625 chr14 107349540 2421719 0.02255919308084599 0.1679336853328951 chr15 102531392 2266032 0.0221008605832641 0.1574908920019457 chr16 90354753 2127772 0.02354908767223347 0.1723651116186194 chr17 81195210 1912224 0.0235509459240268 0.17003765336373253 chr18 78077248 2195011 0.02811332438356434 0.35592386304148077 chr19 59128983 1373704 0.023232329228459754 0.29531317310910216 chr20 63025520 1490549 0.02364992783875484 0.16425026717607355 chr21 48129895 1055029 0.021920450896475048 0.16164287756245324 chr22 51304566 802775 0.015647242781470953 0.1317377154355467 chrMT 16571 6880 0.4151831512883954 0.687008887320299 chrX 155270560 4629391 0.029814995192907142 0.1947624420723783 chrY 59373566 202577 0.0034119055608012494 0.08221271594987639