BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004110.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 = 4,159,493 number of mapped reads = 3,452,768 (83.01%) number of supplementary alignments = 22,027 (0.53%) number of secondary alignments = 0 number of mapped bases = 225,738,628 bp number of sequenced bases = 225,610,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,693 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1677 >>>>>>> ACTG content number of A's = 62,671,029 bp (27.78%) number of C's = 41,318,166 bp (18.31%) number of T's = 71,498,407 bp (31.69%) number of G's = 50,094,053 bp (22.2%) number of N's = 28,558 bp (0.01%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 2,457,625 number of insertions = 21,798 mapped reads with insertion percentage = 0.63% number of deletions = 77,970 mapped reads with deletion percentage = 2.23% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.0729X std coverageData = 0.7916X There is a 5.59% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 18681261 0.07494970694576525 1.4121856780183033 chr2 243199373 17851566 0.07340300996581928 0.9710979857940242 chr3 198022430 15083549 0.0761709115477474 0.35412700055797347 chr4 191154276 13986698 0.07316968415605832 0.36811400166484504 chr5 180915260 14086501 0.07786242575667747 0.35615783397619916 chr6 171115067 13281091 0.07761497121699984 0.45901536139688165 chr7 159138663 14326319 0.09002412568968234 1.490360268347668 chr8 146364022 13983669 0.09554034392413731 0.8264429917433733 chr9 141213431 8330686 0.058993581141725815 0.7880559922945329 chr10 135534747 10965528 0.08090565882710506 0.6719702556352024 chr11 135006516 10324138 0.07647140527646829 0.7278315312777717 chr12 133851895 9752721 0.07286203157601916 0.355409157939308 chr13 115169878 6929934 0.060171410444665056 0.30653417048782805 chr14 107349540 5602368 0.052188095077072526 0.422290921769252 chr15 102531392 5999835 0.05851705397699077 0.3248444822282923 chr16 90354753 6332427 0.07008404970129242 0.4266133009032184 chr17 81195210 5239611 0.06453103575937547 0.4046342281308909 chr18 78077248 6450338 0.08261482269457038 1.6958936562923757 chr19 59128983 3976779 0.0672560020185025 0.9760452171953505 chr20 63025520 4891644 0.0776137031475504 0.39176503172127847 chr21 48129895 3331528 0.06921951523060667 0.3940023142476638 chr22 51304566 2319826 0.04521675517145979 0.26002522859332783 chrMT 16571 106375 6.419347052078933 5.753673158518575 chrX 155270560 13292561 0.08560902337184847 0.4850997285304087 chrY 59373566 611675 0.010302143549875378 0.20971420022533685