BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081165.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,374,232 number of mapped reads = 2,131,241 (89.77%) number of supplementary alignments = 16,971 (0.71%) number of secondary alignments = 0 number of mapped bases = 144,558,202 bp number of sequenced bases = 144,500,943 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,018 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4217 >>>>>>> ACTG content number of A's = 41,392,465 bp (28.65%) number of C's = 26,788,523 bp (18.54%) number of T's = 45,227,950 bp (31.3%) number of G's = 31,048,847 bp (21.49%) number of N's = 43,158 bp (0.03%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,235,908 number of insertions = 11,887 mapped reads with insertion percentage = 0.55% number of deletions = 34,872 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 0.4263X There is a 4.07% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12631857 0.05067934013291786 0.7715110798692021 chr2 243199373 13199919 0.05427612266089189 0.4940027610722426 chr3 198022430 9382643 0.04738171832352527 0.24051508560114992 chr4 191154276 10031073 0.05247632022628675 0.26616300533539666 chr5 180915260 8672400 0.047936254796859035 0.24511937486713717 chr6 171115067 7335210 0.0428671193519154 0.2975545115243995 chr7 159138663 7846622 0.04930682369751969 0.535482723621361 chr8 146364022 7865384 0.05373850685792168 0.6545689949926924 chr9 141213431 5762437 0.04080657880198379 0.4018598532409775 chr10 135534747 6878670 0.050752077620361075 0.40048026420309246 chr11 135006516 6067653 0.044943408509260395 0.365128642220876 chr12 133851895 6677881 0.0498900743990214 0.25376201483690075 chr13 115169878 5132477 0.04456440424465848 0.23279790227974875 chr14 107349540 4491851 0.0418432254111196 0.26165368965564806 chr15 102531392 3946529 0.038490933586466866 0.22349098205930398 chr16 90354753 3926091 0.04345195874753816 0.27674260138948714 chr17 81195210 3789173 0.04666744503770604 0.28599201363630544 chr18 78077248 4027116 0.05157861096743574 0.8006274177294425 chr19 59128983 2612651 0.04418562382512143 0.5651863977990885 chr20 63025520 2850246 0.04522368082008685 0.2532812979164069 chr21 48129895 1679946 0.03490441855316742 0.23291317253798355 chr22 51304566 1357127 0.026452362933934576 0.17808381697434766 chrMT 16571 16201 0.9776718363405951 1.2058524024702038 chrX 155270560 8036385 0.051757300289249936 0.29578664420140305 chrY 59373566 340660 0.00573757015032582 0.1300366795440294