BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124781.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 479,955 number of mapped reads = 479,449 (99.89%) number of supplementary alignments = 223,066 (46.48%) number of secondary alignments = 0 number of mapped bases = 72,078,569 bp number of sequenced bases = 72,032,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 701,069 duplication rate = 40.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 27.4706 >>>>>>> ACTG content number of A's = 20,091,821 bp (27.89%) number of C's = 13,847,395 bp (19.22%) number of T's = 23,285,120 bp (32.33%) number of G's = 14,808,176 bp (20.56%) number of N's = 0 bp (0%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 602,190 number of insertions = 9,817 mapped reads with insertion percentage = 2.03% number of deletions = 43,319 mapped reads with deletion percentage = 8.74% homopolymer indels = 53.67% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 38.1276X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 16346 6.558057883434521E-5 0.04295769102706726 chr2 243199373 10116 4.1595501975245635E-5 0.028747432514159395 chr3 198022430 3637 1.8366606247585184E-5 0.0094894714156968 chr4 191154276 4248 2.2222887653321447E-5 0.006121426112409836 chr5 180915260 4897 2.706792119139093E-5 0.009068443355604932 chr6 171115067 5749 3.359727521831844E-5 0.026422398099715104 chr7 159138663 8658 5.440538356163015E-5 0.058652612876897214 chr8 146364022 52167902 0.35642572052303945 157.65376704319615 chr9 141213431 2380 1.68539209276772E-5 0.004358009137920939 chr10 135534747 19817341 0.1462159441667014 79.76834115104467 chr11 135006516 3353 2.4835838293908717E-5 0.008091829542574591 chr12 133851895 5285 3.948393857255439E-5 0.015103270224359491 chr13 115169878 3311 2.8748836566450126E-5 0.01388810532874137 chr14 107349540 4545 4.233832767238686E-5 0.03955522719872251 chr15 102531392 1560 1.5214852442459768E-5 0.003984699796402174 chr16 90354753 2445 2.706000424792263E-5 0.005457277238369869 chr17 81195210 1660 2.044455578106147E-5 0.00888718595647138 chr18 78077248 893 1.1437390826070099E-5 0.004372866004778437 chr19 59128983 1377 2.3288071773532787E-5 0.007949860004493929 chr20 63025520 1572 2.4942277350508173E-5 0.005960257599404789 chr21 48129895 762 1.583215587733985E-5 0.016241487171295886 chr22 51304566 702 1.3682992659951552E-5 0.0036963920958862587 chrMT 16571 284 0.017138374268300043 0.1293371353291619 chrX 155270560 9343 6.017238554430408E-5 0.019310626548954206 chrY 59373566 203 3.419029943392654E-6 0.0018444988090970916