BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080677.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 = 1,461,957 number of mapped reads = 1,340,421 (91.69%) number of supplementary alignments = 14,200 (0.97%) number of secondary alignments = 0 number of mapped bases = 89,486,231 bp number of sequenced bases = 89,451,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,720 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.807 >>>>>>> ACTG content number of A's = 24,604,069 bp (27.51%) number of C's = 16,445,472 bp (18.38%) number of T's = 28,416,360 bp (31.77%) number of G's = 19,982,054 bp (22.34%) number of N's = 3,937 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 614,199 number of insertions = 6,850 mapped reads with insertion percentage = 0.51% number of deletions = 21,081 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.11% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.231X There is a 2.57% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 11147947 0.04472585446437062 0.2986641570990373 chr2 243199373 6078481 0.02499381854903055 0.3246406676441385 chr3 198022430 5721796 0.02889468632417045 0.18590000029152182 chr4 191154276 3788892 0.019821120820755274 0.15700215289267763 chr5 180915260 4101423 0.022670409339709652 0.16452105773361153 chr6 171115067 5397609 0.031543738927443485 0.2340262335816678 chr7 159138663 5576646 0.035042684755997984 0.3880895432231114 chr8 146364022 10366186 0.07082468668427272 0.3259501712099908 chr9 141213431 2803112 0.019850179831690372 0.17487097872782462 chr10 135534747 4284658 0.03161298556155493 0.20936696782130204 chr11 135006516 3801739 0.02815967045620228 0.20010433779861028 chr12 133851895 2927609 0.021872002633955986 0.16264551611701114 chr13 115169878 1840046 0.015976799072410234 0.1402065948590721 chr14 107349540 1814167 0.01689962528018285 0.14546476588271906 chr15 102531392 1679389 0.016379266556724403 0.14927600430025226 chr16 90354753 2222211 0.02459429002036008 0.1749611058640368 chr17 81195210 1501975 0.018498320282686626 0.15330441865201663 chr18 78077248 2767157 0.035441272212873076 0.26336013767069444 chr19 59128983 1456258 0.02462849733099587 0.2088120534814819 chr20 63025520 2253605 0.03575702350412976 0.20943269678871915 chr21 48129895 1309421 0.027205980815042292 0.18436185531189933 chr22 51304566 902295 0.017587031142608244 0.1442716556556853 chrMT 16571 14431 0.870858729105063 1.0769277469557919 chrX 155270560 5557287 0.035790989611939314 0.21363785254277595 chrY 59373566 171891 0.002895076236451757 0.062367155614677726