BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716300.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,396,473 number of mapped reads = 1,277,595 (91.49%) number of supplementary alignments = 6,445 (0.46%) number of secondary alignments = 0 number of mapped bases = 75,491,607 bp number of sequenced bases = 75,469,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,880 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5068 >>>>>>> ACTG content number of A's = 19,072,494 bp (25.27%) number of C's = 14,478,249 bp (19.18%) number of T's = 23,788,321 bp (31.52%) number of G's = 18,128,515 bp (24.02%) number of N's = 2,174 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 372,132 number of insertions = 5,252 mapped reads with insertion percentage = 0.41% number of deletions = 13,525 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.227X There is a 2.2% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 6276141 0.02518004157750925 0.3848777135085116 chr2 243199373 6408604 0.026351235699937435 0.28720584180254155 chr3 198022430 4986466 0.025181319106123482 0.1727728394779529 chr4 191154276 4876168 0.025509071008173522 0.18501571837883732 chr5 180915260 4286181 0.023691649891778063 0.16757056359802114 chr6 171115067 4119523 0.024074577839483885 0.19058694581216273 chr7 159138663 3967851 0.024933293551674493 0.2652625001047204 chr8 146364022 3830977 0.026174308055021883 0.2238392286234595 chr9 141213431 3370591 0.023868770669554795 0.20220293946290158 chr10 135534747 3710751 0.027378595394434168 0.23262266475377136 chr11 135006516 3619412 0.02680916527021555 0.20878656441584817 chr12 133851895 3327399 0.024858811300355516 0.17326844826301888 chr13 115169878 2376146 0.020631662039270374 0.1558451480773299 chr14 107349540 2167561 0.02019161889282432 0.16105943682454676 chr15 102531392 2237174 0.021819405319299674 0.16088951980757943 chr16 90354753 2238278 0.02477211132434837 0.17971702741767756 chr17 81195210 2059745 0.025367814185097863 0.1812423128765971 chr18 78077248 2048040 0.02623094502511154 0.31815219100366515 chr19 59128983 1565366 0.026473751459584548 0.2808451712978067 chr20 63025520 1552679 0.024635718991291147 0.17362496327899124 chr21 48129895 988905 0.02054658544341308 0.16768546381005145 chr22 51304566 918745 0.017907665372317933 0.14525700075664164 chrMT 16571 29864 1.8021845392553255 1.6481122090240565 chrX 155270560 4290649 0.027633371065319788 0.19152972350815145 chrY 59373566 238391 0.004015103286873488 0.11247884273052239