BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 614,302 number of mapped reads = 46,148 (7.51%) number of supplementary alignments = 918 (0.15%) number of secondary alignments = 0 number of mapped bases = 4,274,208 bp number of sequenced bases = 4,223,450 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,081 duplication rate = 36.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.5678 >>>>>>> ACTG content number of A's = 679,858 bp (16.1%) number of C's = 459,596 bp (10.88%) number of T's = 604,455 bp (14.31%) number of G's = 2,479,457 bp (58.71%) number of N's = 84 bp (0%) GC percentage = 69.59% >>>>>>> Mismatches and indels general error rate = 0.035 number of mismatches = 128,822 number of insertions = 4,341 mapped reads with insertion percentage = 7.63% number of deletions = 8,326 mapped reads with deletion percentage = 17.32% homopolymer indels = 33.5% >>>>>>> Coverage mean coverageData = 0.0014X std coverageData = 2.3516X There is a 0.01% 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 136303 5.468511952072528E-4 0.20545719448270114 chr2 243199373 2267953 0.009325488680433399 8.362595030006686 chr3 198022430 84171 4.2505790884396277E-4 0.16895203478989446 chr4 191154276 83593 4.373064613004001E-4 0.1332993955229945 chr5 180915260 122347 6.762668887080062E-4 0.15895168201855914 chr6 171115067 99798 5.832215815337875E-4 0.16130697153469314 chr7 159138663 97766 6.14344736577308E-4 0.3138533204132289 chr8 146364022 120273 8.217388286856452E-4 0.19147572261913368 chr9 141213431 49379 3.496763703730136E-4 0.08405516689615812 chr10 135534747 46883 3.4591129608999824E-4 0.10121937881120215 chr11 135006516 120870 8.952901206635093E-4 0.21222057411305809 chr12 133851895 72588 5.42300876651765E-4 0.12143465675711149 chr13 115169878 52735 4.5788882402046134E-4 0.13101050264568073 chr14 107349540 143399 0.0013358138283592086 0.3138439849380012 chr15 102531392 72963 7.116162043328154E-4 0.21093328256802577 chr16 90354753 70708 7.825598283689625E-4 0.2616461469389664 chr17 81195210 46615 5.741102215266147E-4 0.1484155561562623 chr18 78077248 92645 0.0011865812688480004 0.23492008189659944 chr19 59128983 19934 3.3712739486826623E-4 0.09343911840208241 chr20 63025520 41962 6.657937927366565E-4 0.15470251827916912 chr21 48129895 21530 4.473311234109279E-4 0.09731841288083963 chr22 51304566 6291 1.226206649911043E-4 0.03354584924034032 chrMT 16571 9496 0.5730493029992155 3.92040804311104 chrX 155270560 384536 0.002476554473687736 0.355816006382039 chrY 59373566 9470 1.5949858898486912E-4 0.06704831856244754