BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084797.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 = 1,823,882 number of mapped reads = 1,637,109 (89.76%) number of supplementary alignments = 21,765 (1.19%) number of secondary alignments = 0 number of mapped bases = 109,028,676 bp number of sequenced bases = 108,987,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,473 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.441 >>>>>>> ACTG content number of A's = 29,845,165 bp (27.38%) number of C's = 20,451,391 bp (18.76%) number of T's = 34,162,409 bp (31.35%) number of G's = 24,511,787 bp (22.49%) number of N's = 16,354 bp (0.02%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 844,133 number of insertions = 8,949 mapped reads with insertion percentage = 0.54% number of deletions = 25,426 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.0352X std coverageData = 0.2711X There is a 2.99% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% 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% 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 8396670 0.033687659297747544 0.3143755153913837 chr2 243199373 9076922 0.03732296628906194 0.45067233398375467 chr3 198022430 7417537 0.037458064725294 0.22113509571721643 chr4 191154276 6233499 0.03260978059418352 0.2100748674636126 chr5 180915260 6116938 0.03381106712612303 0.21116946953600646 chr6 171115067 6379798 0.03728367181131981 0.23960740385523746 chr7 159138663 6578198 0.04133626534238257 0.2755671824040331 chr8 146364022 6443055 0.04402075668568332 0.3340427109558123 chr9 141213431 7970905 0.056445799408414626 0.3293958425526187 chr10 135534747 3718574 0.027436314910448758 0.21286396695957885 chr11 135006516 4388836 0.032508327227702104 0.23456936091211114 chr12 133851895 4921295 0.03676671891720323 0.2232529178163277 chr13 115169878 2742729 0.023814638407448865 0.1777556881502934 chr14 107349540 2346374 0.021857327008574047 0.17829461471089142 chr15 102531392 2855574 0.027850728877259368 0.1938859796261924 chr16 90354753 2287243 0.025314030795922822 0.1952426249005419 chr17 81195210 3309992 0.040765853059558564 0.23428044704852558 chr18 78077248 4961171 0.06354182719145018 0.42909398567864265 chr19 59128983 2163021 0.036581400359955454 0.27029317435838823 chr20 63025520 2032163 0.03224349438132363 0.21053986656740847 chr21 48129895 969171 0.020136570004983388 0.16763579786550667 chr22 51304566 1046299 0.020393876833496652 0.16171449569911486 chrMT 16571 24027 1.4499426709311447 1.4687443703376506 chrX 155270560 6411727 0.04129390014436735 0.25020162273213153 chrY 59373566 236958 0.003990967967125303 0.09095298551772063