BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124809.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 = 767,471 number of mapped reads = 766,436 (99.87%) number of supplementary alignments = 288,010 (37.53%) number of secondary alignments = 0 number of mapped bases = 113,892,751 bp number of sequenced bases = 113,824,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,052,543 duplication rate = 32.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4193 >>>>>>> ACTG content number of A's = 32,817,015 bp (28.83%) number of C's = 21,210,023 bp (18.63%) number of T's = 36,358,517 bp (31.94%) number of G's = 23,438,801 bp (20.59%) number of N's = 0 bp (0%) GC percentage = 39.23% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 971,085 number of insertions = 16,914 mapped reads with insertion percentage = 2.18% number of deletions = 63,735 mapped reads with deletion percentage = 7.86% homopolymer indels = 79.22% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 67.2773X 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 14425 5.787347667230085E-5 0.013569546947817696 chr2 243199373 48819 2.0073653726072722E-4 0.15825258714859866 chr3 198022430 7764 3.920767965527946E-5 0.007396924317991355 chr4 191154276 23709 1.2403070700861538E-4 0.22035423695594675 chr5 180915260 7721 4.2677439150240835E-5 0.00885871943223167 chr6 171115067 7748 4.527947267203536E-5 0.012082042311244046 chr7 159138663 8528 5.358848591055462E-5 0.024280954614210322 chr8 146364022 110634670 0.7558870580913662 309.10905949237485 chr9 141213431 4870 3.448680458730586E-5 0.005954475576250981 chr10 135534747 3077985 0.022709932826303205 14.086491677113099 chr11 135006516 4231 3.1339228100664414E-5 0.005681455953734167 chr12 133851895 7016 5.241614248345158E-5 0.02206397292599355 chr13 115169878 4411 3.829994506028738E-5 0.009832690689764776 chr14 107349540 4392 4.091307703787087E-5 0.007995020502442074 chr15 102531392 3783 3.689601717296494E-5 0.009298385232908326 chr16 90354753 4220 4.6704792607866464E-5 0.006928026383118939 chr17 81195210 3686 4.539676663192324E-5 0.006931281249223829 chr18 78077248 2696 3.452990556224523E-5 0.005876113787859037 chr19 59128983 2920 4.938356541664178E-5 0.00711090565791116 chr20 63025520 3542 5.61994569818702E-5 0.007564894961715615 chr21 48129895 1566 3.253695026760395E-5 0.006546916477965451 chr22 51304566 3526 6.872682638032647E-5 0.026408314799416542 chrMT 16571 234 0.014121054854866937 0.11799004476926338 chrX 155270560 7044 4.536597278969046E-5 0.01894687882582402 chrY 59373566 3245 5.465395155817321E-5 0.007665542934897442