BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084259.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 = 2,082,603 number of mapped reads = 1,783,769 (85.65%) number of supplementary alignments = 12,036 (0.58%) number of secondary alignments = 0 number of mapped bases = 112,025,733 bp number of sequenced bases = 111,990,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,045 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0808 >>>>>>> ACTG content number of A's = 32,127,744 bp (28.69%) number of C's = 21,444,144 bp (19.15%) number of T's = 34,023,462 bp (30.38%) number of G's = 24,393,882 bp (21.78%) number of N's = 1,206 bp (0%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 923,511 number of insertions = 7,967 mapped reads with insertion percentage = 0.44% number of deletions = 22,425 mapped reads with deletion percentage = 1.25% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.2561X There is a 3.17% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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 8710560 0.03494699417418904 0.3052608545488208 chr2 243199373 9510722 0.039106687992982614 0.3210553114389446 chr3 198022430 7836602 0.03957431488947995 0.22108181166301422 chr4 191154276 7344165 0.038420092679485755 0.22289227147882507 chr5 180915260 7099693 0.0392431959581519 0.22056894708273347 chr6 171115067 6772359 0.039577806435946404 0.25195789731279095 chr7 159138663 6040512 0.03795753895456568 0.2773653401345795 chr8 146364022 5648439 0.03859171757387208 0.2779587257205655 chr9 141213431 4845189 0.03431110600237452 0.25231295610511145 chr10 135534747 5277202 0.038936155611815175 0.26005297561479385 chr11 135006516 5061989 0.037494405084862716 0.24785490416345918 chr12 133851895 4936606 0.036881106539433 0.2149565170517442 chr13 115169878 3801422 0.03300708541169072 0.20294906920058423 chr14 107349540 3428688 0.03193947547423119 0.20995549456734586 chr15 102531392 3091767 0.030154345315042637 0.20002468710412538 chr16 90354753 2929221 0.032419113580001706 0.21387237402636539 chr17 81195210 2754324 0.03392224738380503 0.2211245310364285 chr18 78077248 3179826 0.040726665980850146 0.4771346301126854 chr19 59128983 1912455 0.03234378308180948 0.25935733338081585 chr20 63025520 2250863 0.03571351731806417 0.2162257590767086 chr21 48129895 1450557 0.03013837865218696 0.20041056348798794 chr22 51304566 1078429 0.021020136882163667 0.16010991989104562 chrMT 16571 25282 1.5256773882083157 1.4337906598661763 chrX 155270560 6775703 0.04363804059185463 0.24717822921718696 chrY 59373566 263158 0.004432241782479428 0.0916524428936342