BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230380.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 = 3,996,728 number of mapped reads = 3,457,685 (86.51%) number of supplementary alignments = 43,346 (1.08%) number of secondary alignments = 0 number of mapped bases = 222,310,961 bp number of sequenced bases = 222,219,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 985,069 duplication rate = 15.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5857 >>>>>>> ACTG content number of A's = 59,720,427 bp (26.87%) number of C's = 40,873,894 bp (18.39%) number of T's = 70,351,402 bp (31.66%) number of G's = 51,159,714 bp (23.02%) number of N's = 113,646 bp (0.05%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,880,255 number of insertions = 17,387 mapped reads with insertion percentage = 0.5% number of deletions = 56,383 mapped reads with deletion percentage = 1.61% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0718X std coverageData = 0.788X There is a 2.04% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.17% 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 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% 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% 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 21134627 0.08479267540119789 0.8967124914230321 chr2 243199373 30475107 0.1253091511876554 1.1390264276688111 chr3 198022430 13724464 0.06930762338387626 0.6931111814556536 chr4 191154276 16223254 0.08486995080350701 0.7760114894584464 chr5 180915260 10827042 0.05984593007798237 0.6425691579844028 chr6 171115067 9725114 0.05683376788789733 0.6390649416460987 chr7 159138663 8554288 0.053753675183258263 0.9846402879089428 chr8 146364022 7960050 0.05438529148918851 0.8461626880364481 chr9 141213431 8241274 0.05836041190727814 0.6973205306089569 chr10 135534747 16887615 0.124599893191965 0.9583059566386334 chr11 135006516 11597116 0.08590041683617701 0.7881762983992181 chr12 133851895 6063586 0.04530071090887432 0.5530556734089143 chr13 115169878 6260926 0.054362530452624076 0.6183212607969787 chr14 107349540 7524774 0.07009600600058463 0.7248560502797228 chr15 102531392 5226491 0.05097454445951539 0.598961184082847 chr16 90354753 5148254 0.05697823112858269 0.6258343809839598 chr17 81195210 7990830 0.09841504197107194 0.8252519462809645 chr18 78077248 3895598 0.04989415098237069 0.9324968865093144 chr19 59128983 4903266 0.08292491687198476 0.7778924614893388 chr20 63025520 6012281 0.09539438944732229 0.8181742699808392 chr21 48129895 2929855 0.060873912149610965 0.6551358722577588 chr22 51304566 2302514 0.044879319318284455 0.5341480630380905 chrMT 16571 30798 1.858548065898256 3.9510751710214245 chrX 155270560 8198950 0.05280427918853387 0.6220151932074247 chrY 59373566 472887 0.007964604989365133 0.2250824987199187