BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237815.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 = 1,563,347 number of mapped reads = 1,458,558 (93.3%) number of supplementary alignments = 11,159 (0.71%) number of secondary alignments = 0 number of mapped bases = 101,376,496 bp number of sequenced bases = 101,328,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,357 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5152 >>>>>>> ACTG content number of A's = 31,003,252 bp (30.6%) number of C's = 19,783,910 bp (19.52%) number of T's = 30,011,093 bp (29.62%) number of G's = 20,368,302 bp (20.1%) number of N's = 161,927 bp (0.16%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 903,982 number of insertions = 7,371 mapped reads with insertion percentage = 0.5% number of deletions = 26,984 mapped reads with deletion percentage = 1.83% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.4511X There is a 1.48% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% 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 0.01% 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% 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 8427268 0.03381041927273674 0.814121540399171 chr2 243199373 10358664 0.042593300600326796 0.45576207271297964 chr3 198022430 9195802 0.04643818379564375 0.4233234899403662 chr4 191154276 5014673 0.02623364281947844 0.32425305117313846 chr5 180915260 8504956 0.04701071650893352 0.4256914494910779 chr6 171115067 5610586 0.032788380931995896 0.37642252130740766 chr7 159138663 5639263 0.03543615921920872 0.49992894076658817 chr8 146364022 5040444 0.034437725413148323 0.4562316229146539 chr9 141213431 4170762 0.02953516510763059 0.38178589099407795 chr10 135534747 4154571 0.030653180029177315 0.42343443862784974 chr11 135006516 5118381 0.037912103442473845 0.5108815407512249 chr12 133851895 4313586 0.03222655906365764 0.34783840990119785 chr13 115169878 3097433 0.026894471486719817 0.316104768369488 chr14 107349540 2401898 0.02237455325844899 0.2884385189361128 chr15 102531392 1845877 0.018003042424314303 0.25523152764816365 chr16 90354753 1916012 0.02120543675217617 0.2948434397612003 chr17 81195210 1918362 0.023626541516426892 0.33472694384737345 chr18 78077248 2002611 0.025649098185427845 0.5572172342607611 chr19 59128983 1312801 0.022202326733744095 0.42788475242910445 chr20 63025520 1671649 0.0265233670424298 0.31831278608340285 chr21 48129895 1292321 0.026850692277637422 0.3253854158683919 chr22 51304566 639561 0.01246596647947475 0.2078418186709075 chrMT 16571 345303 20.837788908333835 16.511868102181168 chrX 155270560 7112010 0.04580398241624169 0.43076850395313204 chrY 59373566 271702 0.004576144205318575 0.1622010806427203