BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004131.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 = 2,354,880 number of mapped reads = 2,151,289 (91.35%) number of supplementary alignments = 26,203 (1.11%) number of secondary alignments = 0 number of mapped bases = 144,282,758 bp number of sequenced bases = 144,217,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,625 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1094 >>>>>>> ACTG content number of A's = 41,143,081 bp (28.53%) number of C's = 27,252,986 bp (18.9%) number of T's = 43,200,314 bp (29.95%) number of G's = 32,591,610 bp (22.6%) number of N's = 29,793 bp (0.02%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,215,146 number of insertions = 12,807 mapped reads with insertion percentage = 0.59% number of deletions = 38,968 mapped reads with deletion percentage = 1.79% homopolymer indels = 43.75% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.519X There is a 4.22% of reference with a coverageData >= 1X There is a 0.27% 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 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11162713 0.044785096041947275 1.1159326922974036 chr2 243199373 11379994 0.046792859124682035 0.5010499718970964 chr3 198022430 9624256 0.04860184778057718 0.23931148124139284 chr4 191154276 9226147 0.04826544921234197 0.2417069942090558 chr5 180915260 7733784 0.04274810206723302 0.22671090320736845 chr6 171115067 8702121 0.050855375581859194 0.2849319118188744 chr7 159138663 8973919 0.0563905642464773 0.7894608333317632 chr8 146364022 9043527 0.06178790987309709 0.5726014159763363 chr9 141213431 4771201 0.0337871615059052 0.4301409269474764 chr10 135534747 6777590 0.05000629100668923 0.5067412313511049 chr11 135006516 6718877 0.04976705716929989 0.43744884087609204 chr12 133851895 6571411 0.049094643000758414 0.24273299826359251 chr13 115169878 4705791 0.04085956399120263 0.21389983430901338 chr14 107349540 3976355 0.03704119272425387 0.2487062901720854 chr15 102531392 3953956 0.03856336993844773 0.21569308080586494 chr16 90354753 3180837 0.03520387023801615 0.2786502899155895 chr17 81195210 3464657 0.04267070680647295 0.2558183830311084 chr18 78077248 3995196 0.05116978508258898 1.009236592083485 chr19 59128983 2437326 0.04122049587763077 0.7753017568599985 chr20 63025520 3172222 0.05033234156576574 0.25673844394598966 chr21 48129895 1560487 0.032422406074228916 0.2250534358289069 chr22 51304566 1746775 0.03404716453502404 0.19385090803812022 chrMT 16571 156204 9.426347233118097 6.602206456286184 chrX 155270560 10845488 0.06984896557338365 0.34984124198462385 chrY 59373566 401924 0.006769409807724872 0.11797616498575517