BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524587.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,731,928 number of mapped reads = 2,543,434 (93.1%) number of supplementary alignments = 5,697 (0.21%) number of secondary alignments = 0 number of mapped bases = 148,954,954 bp number of sequenced bases = 148,907,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,577 duplication rate = 5.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4745 >>>>>>> ACTG content number of A's = 38,299,566 bp (25.72%) number of C's = 30,199,322 bp (20.28%) number of T's = 45,289,217 bp (30.41%) number of G's = 35,118,061 bp (23.58%) number of N's = 934 bp (0%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 705,633 number of insertions = 8,890 mapped reads with insertion percentage = 0.35% number of deletions = 28,082 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.4017X There is a 3.97% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15662406 0.06283798185602113 0.7328810771965851 chr2 243199373 13329976 0.054810897888293485 0.46277973321163113 chr3 198022430 9656154 0.0487629305427673 0.2599049481096022 chr4 191154276 6762921 0.035379386438627196 0.2661524894344407 chr5 180915260 9409523 0.05201066510365129 0.26930053095527584 chr6 171115067 9761210 0.05704471366042828 0.3129424011555905 chr7 159138663 9213464 0.05789582384514566 0.5579282074091808 chr8 146364022 13522608 0.09239024601278038 0.5427365070419328 chr9 141213431 5573653 0.039469708798449916 0.36236981879117136 chr10 135534747 6532317 0.04819662222854188 0.39535912739191487 chr11 135006516 7690932 0.05696711705381687 0.39292829994405987 chr12 133851895 4658215 0.034801262992952026 0.23022724354623447 chr13 115169878 3720454 0.032304054363937074 0.21391132903870327 chr14 107349540 2758154 0.025693207441783168 0.20581977101916507 chr15 102531392 3891202 0.03795132323961817 0.24263016453337355 chr16 90354753 4437581 0.04911286736625798 0.28148720718622294 chr17 81195210 3346881 0.04122017788980409 0.25069554387323706 chr18 78077248 3498615 0.0448096608118155 0.5885681867115811 chr19 59128983 2991316 0.05058967444104357 0.5336154778628254 chr20 63025520 2822433 0.04478238339009341 0.2582897253821536 chr21 48129895 1330910 0.027652460077047747 0.22648843860681295 chr22 51304566 2627841 0.05122041184404522 0.267841892231341 chrMT 16571 38781 2.340293283446986 2.0757742507412487 chrX 155270560 5361259 0.034528496580420655 0.2735454489992789 chrY 59373566 356148 0.005998426976745847 0.16537622910364908