BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234124.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,299,814 number of mapped reads = 3,883,422 (90.32%) number of supplementary alignments = 39,755 (0.92%) number of secondary alignments = 0 number of mapped bases = 269,316,427 bp number of sequenced bases = 269,244,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,114,177 duplication rate = 11.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.196 >>>>>>> ACTG content number of A's = 64,319,337 bp (23.89%) number of C's = 44,616,713 bp (16.57%) number of T's = 68,801,190 bp (25.55%) number of G's = 91,449,339 bp (33.97%) number of N's = 57,906 bp (0.02%) GC percentage = 50.54% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,341,540 number of insertions = 14,120 mapped reads with insertion percentage = 0.36% number of deletions = 45,615 mapped reads with deletion percentage = 1.16% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.087X std coverageData = 84.5897X There is a 2.13% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 19061849 0.07647663593985589 0.7230202941488535 chr2 243199373 45379031 0.18659189141906218 301.78595049460847 chr3 198022430 72518941 0.3662157918171189 1.6227036292731818 chr4 191154276 3623040 0.018953486554493817 0.3246219019089882 chr5 180915260 2957715 0.016348620895771864 0.30263593133137334 chr6 171115067 2677592 0.015647903173833314 0.42260384244835975 chr7 159138663 2359038 0.014823789238445469 0.3226910621408748 chr8 146364022 2347295 0.016037376999656378 0.3039140732139008 chr9 141213431 1815849 0.012858897253193996 0.263513379285732 chr10 135534747 6244089 0.046070023652311096 0.5680000645000091 chr11 135006516 1988631 0.014729889037355797 0.4552986460584307 chr12 133851895 30392322 0.2270593330038398 1.299773353660274 chr13 115169878 1502681 0.013047517511479869 0.2666106617799217 chr14 107349540 1516296 0.014124848602052697 0.422616150273797 chr15 102531392 1792183 0.017479358906977483 0.4445111518951919 chr16 90354753 1086844 0.012028631188887208 0.24707550150416155 chr17 81195210 1219912 0.015024433091557987 0.3037929697576832 chr18 78077248 1306376 0.016731839728777325 0.3722780788508756 chr19 59128983 1584137 0.026791209989185844 0.39852737034323304 chr20 63025520 850838 0.013499896549842032 0.29286625186099 chr21 48129895 2874656 0.05972703659544655 0.6353542253152051 chr22 51304566 427784 0.00833812725362495 0.20367940201038423 chrMT 16571 85768 5.175789029026613 5.255677331823531 chrX 155270560 62749918 0.4041327473797995 1.6974232228524744 chrY 59373566 953642 0.016061726863432796 0.26007457838968884