BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818875.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,512,167 number of mapped reads = 1,471,322 (97.3%) number of supplementary alignments = 22,202 (1.47%) number of secondary alignments = 0 number of mapped bases = 136,197,853 bp number of sequenced bases = 136,111,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 305,658 duplication rate = 17.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3392 >>>>>>> ACTG content number of A's = 38,838,060 bp (28.53%) number of C's = 30,063,890 bp (22.09%) number of T's = 39,203,557 bp (28.8%) number of G's = 28,004,227 bp (20.57%) number of N's = 1,847 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 822,376 number of insertions = 19,941 mapped reads with insertion percentage = 1.31% number of deletions = 44,786 mapped reads with deletion percentage = 2.97% homopolymer indels = 41.54% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.5286X There is a 3.12% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.23% 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% 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 13055103 0.052377414136914026 0.7939175946892184 chr2 243199373 10308032 0.04238510927410985 0.7570798505316314 chr3 198022430 8501767 0.04293335355999823 0.271330761977166 chr4 191154276 6905081 0.036123078931281666 0.31490561420182456 chr5 180915260 6018426 0.03326654700106558 0.25186815940927254 chr6 171115067 6754802 0.03947520296386291 0.2904332579995985 chr7 159138663 12260110 0.07704042354559684 1.1340091352446777 chr8 146364022 11768548 0.08040601671905409 0.46981188162587567 chr9 141213431 4968080 0.03518135608503132 0.4418638579519096 chr10 135534747 6234354 0.04599819705274545 0.646567768991976 chr11 135006516 6015550 0.044557478988643776 0.3363666019028715 chr12 133851895 5320530 0.03974938120973184 0.2624640143971362 chr13 115169878 4146125 0.036000081549100886 0.24695491555584093 chr14 107349540 4031584 0.037555670941859645 0.2735824180743752 chr15 102531392 3759213 0.03666401993254905 0.2510619277527636 chr16 90354753 3339771 0.036962870121508715 0.5635036774265427 chr17 81195210 3363842 0.04142906952269721 0.3443236900395194 chr18 78077248 2632011 0.03371034542610928 0.46709780295332143 chr19 59128983 2373195 0.04013590086607781 0.6421969454940353 chr20 63025520 5570297 0.08838161113149086 0.420560818579647 chr21 48129895 1317911 0.027382378457297695 0.24898951477248987 chr22 51304566 1235647 0.024084542494716747 0.2248448661030752 chrMT 16571 338353 20.418381509866634 12.901973419341559 chrX 155270560 5508268 0.03547528906960856 0.2996745465114709 chrY 59373566 471253 0.007937084324697627 0.594583499597459