BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068075.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 = 5,184,156 number of mapped reads = 4,895,382 (94.43%) number of supplementary alignments = 40,519 (0.78%) number of secondary alignments = 0 number of mapped bases = 314,995,488 bp number of sequenced bases = 314,867,694 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 873,580 duplication rate = 14.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7883 >>>>>>> ACTG content number of A's = 82,253,232 bp (26.12%) number of C's = 56,522,645 bp (17.95%) number of T's = 102,726,811 bp (32.63%) number of G's = 73,328,437 bp (23.29%) number of N's = 36,569 bp (0.01%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,724,152 number of insertions = 19,415 mapped reads with insertion percentage = 0.39% number of deletions = 73,709 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.1018X std coverageData = 1.1712X There is a 6.37% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 25224142 0.10119991636851328 2.677029092075604 chr2 243199373 41269300 0.16969328288523178 1.8333112737315709 chr3 198022430 22175711 0.11198585432973426 0.49814889660453443 chr4 191154276 17182770 0.08988954032082443 0.46251074202416614 chr5 180915260 17267989 0.09544794065464682 0.46786876486567097 chr6 171115067 11941786 0.06978804502352794 0.6211891562323948 chr7 159138663 24286173 0.15261013597933773 1.3805222022931356 chr8 146364022 19636880 0.13416466513881398 1.2903799761907135 chr9 141213431 11088216 0.07852097298025426 0.718029227962839 chr10 135534747 17039996 0.12572418790880246 0.8192828238007751 chr11 135006516 15837371 0.11730819718360853 1.0664938745342651 chr12 133851895 16066749 0.12003378061999048 0.5639820080386125 chr13 115169878 8002959 0.0694882997097557 0.45030970300189205 chr14 107349540 6319585 0.05886923222959316 0.4612291320678095 chr15 102531392 6231804 0.060779473275852924 0.42328204310660034 chr16 90354753 6402372 0.0708581650375382 0.456417635806544 chr17 81195210 8264025 0.10177971089673886 0.58721646240815 chr18 78077248 7464341 0.0956019991893157 1.3953337251101274 chr19 59128983 6156197 0.10411471139288832 1.6553689019683204 chr20 63025520 6336661 0.10054119347210463 0.4993800600860357 chr21 48129895 3808525 0.07913013315320966 0.4537584497483998 chr22 51304566 1670178 0.03255417851112901 0.2551241497370233 chrMT 16571 644810 38.911954619516024 20.618584871267238 chrX 155270560 13956524 0.0898851913717578 0.5420129591503939 chrY 59373566 720424 0.012133749891323691 0.2865722590972537