BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714164.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 = 922,480 number of mapped reads = 268,850 (29.14%) number of supplementary alignments = 8,069 (0.87%) number of secondary alignments = 0 number of mapped bases = 35,163,314 bp number of sequenced bases = 34,240,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,933 duplication rate = 42.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.278 >>>>>>> ACTG content number of A's = 9,406,092 bp (27.47%) number of C's = 7,183,218 bp (20.98%) number of T's = 8,977,578 bp (26.22%) number of G's = 8,673,494 bp (25.33%) number of N's = 224 bp (0%) GC percentage = 46.31% >>>>>>> Mismatches and indels general error rate = 0.0489 number of mismatches = 1,572,510 number of insertions = 38,457 mapped reads with insertion percentage = 13.71% number of deletions = 144,991 mapped reads with deletion percentage = 49.76% homopolymer indels = 30.39% >>>>>>> Coverage mean coverageData = 0.0114X std coverageData = 2.1843X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 2528714 0.010145266598954632 1.2904637892726123 chr2 243199373 3909397 0.016074864633799858 5.677198942020317 chr3 198022430 1918880 0.009690215396306368 1.7983908893561131 chr4 191154276 1114883 0.005832372800282009 0.7541887049690362 chr5 180915260 1932372 0.010681089035828156 1.6497834736998913 chr6 171115067 1490908 0.008712897269297741 1.2379829805411804 chr7 159138663 1298248 0.008157967243950013 1.0101101384532565 chr8 146364022 1798836 0.012290151469054328 2.3174952447284936 chr9 141213431 1186799 0.008404292648338812 1.1593424250293098 chr10 135534747 1859526 0.01371992084066826 1.6166252275433943 chr11 135006516 1702388 0.012609672854605033 1.842093641710723 chr12 133851895 1697549 0.01268229336611185 2.0779299871129657 chr13 115169878 1034552 0.008982834904105742 1.3845932703538444 chr14 107349540 1248611 0.011631265490285286 1.529911748481521 chr15 102531392 976404 0.00952297614373557 0.9286017613605044 chr16 90354753 948474 0.010497223095723587 1.145605189428307 chr17 81195210 1204816 0.014838510793924913 2.5945773864673303 chr18 78077248 875392 0.011211870582323803 1.3556763037153179 chr19 59128983 797431 0.01348629655950619 1.439277938183689 chr20 63025520 854889 0.013564172100444392 1.6870554352117566 chr21 48129895 335255 0.006965629158343271 1.3059016146801008 chr22 51304566 379792 0.007402693943459145 0.8377331375283495 chrMT 16571 36626 2.2102468167280187 13.598523914019946 chrX 155270560 3871115 0.02493141649002876 2.0897089481197604 chrY 59373566 161457 0.0027193414658637817 0.47673728526634174