BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008833.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 = 1,552,434 number of mapped reads = 1,392,461 (89.7%) number of supplementary alignments = 10,177 (0.66%) number of secondary alignments = 0 number of mapped bases = 91,596,850 bp number of sequenced bases = 91,556,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,583 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5276 >>>>>>> ACTG content number of A's = 25,742,181 bp (28.12%) number of C's = 16,650,102 bp (18.19%) number of T's = 29,052,296 bp (31.73%) number of G's = 20,095,701 bp (21.95%) number of N's = 16,413 bp (0.02%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 671,042 number of insertions = 8,003 mapped reads with insertion percentage = 0.57% number of deletions = 24,562 mapped reads with deletion percentage = 1.74% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.3045X There is a 2.62% of reference with a coverageData >= 1X There is a 0.24% 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% of reference with a coverageData >= 5X There is a 0% 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 6217435 0.024944511572550905 0.5646979080901665 chr2 243199373 10435088 0.042907544831540335 0.3425341761827782 chr3 198022430 7799063 0.039384745455350686 0.21869252629103297 chr4 191154276 6937034 0.03629023710670223 0.213588068779974 chr5 180915260 3258283 0.01800999539784538 0.14761280053565168 chr6 171115067 4852585 0.028358607369157036 0.2229720290648066 chr7 159138663 4659257 0.02927796999274777 0.31940908758087916 chr8 146364022 8110321 0.05541198505736608 0.5290190810983189 chr9 141213431 3076695 0.02178755220528563 0.2589541654894461 chr10 135534747 6175608 0.04556475838627566 0.3609226542758987 chr11 135006516 3614165 0.026770300479422787 0.22397680524941185 chr12 133851895 3711623 0.02772932725382782 0.18512002970034194 chr13 115169878 785758 0.006822599916273246 0.09062618289703793 chr14 107349540 3392262 0.03160015403885289 0.20161223167816697 chr15 102531392 1479235 0.014427142469693574 0.1295553033723569 chr16 90354753 2753816 0.030477821128015257 0.21070858857493013 chr17 81195210 3084903 0.037993657507628835 0.2620285472317283 chr18 78077248 856350 0.010967983912547738 0.44125754844418125 chr19 59128983 1575347 0.026642551927537804 0.37656760876638995 chr20 63025520 2247598 0.035661712906137066 0.20953899507540347 chr21 48129895 1040858 0.02162601850679292 0.16835337177714219 chr22 51304566 1249234 0.024349372724447177 0.1682256606675366 chrMT 16571 76138 4.594653309999397 3.288280518757606 chrX 155270560 3982352 0.025647824030518084 0.18812539112119253 chrY 59373566 225842 0.0038037466033284915 0.0946869506998945