BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013233.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 = 2,457,933 number of mapped reads = 2,180,524 (88.71%) number of supplementary alignments = 18,598 (0.76%) number of secondary alignments = 0 number of mapped bases = 147,555,611 bp number of sequenced bases = 147,500,125 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,379 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7993 >>>>>>> ACTG content number of A's = 41,054,756 bp (27.83%) number of C's = 27,338,069 bp (18.53%) number of T's = 46,850,289 bp (31.76%) number of G's = 32,224,743 bp (21.85%) number of N's = 32,268 bp (0.02%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,169,529 number of insertions = 10,253 mapped reads with insertion percentage = 0.47% number of deletions = 32,621 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.5444X There is a 3.85% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 10674215 0.042825229310060574 1.0146021882846568 chr2 243199373 14664885 0.06029984707238534 0.559305110572073 chr3 198022430 7513941 0.03794489846428003 0.22980127551981364 chr4 191154276 14878064 0.07783275536038754 0.34370176434434596 chr5 180915260 8653864 0.04783379798918013 0.2607973998055109 chr6 171115067 13963166 0.081601031661344 0.4675890064374622 chr7 159138663 4551525 0.028601000625473397 0.6272043729366596 chr8 146364022 8002999 0.05467873108870976 0.8962401507285462 chr9 141213431 2540153 0.017988041095042866 0.37266597214734976 chr10 135534747 8623306 0.06362431915706457 0.5829266198687356 chr11 135006516 5256927 0.03893832057706015 0.350362671496601 chr12 133851895 6695426 0.05002115210994958 0.27294407305930085 chr13 115169878 3432739 0.029805875109114904 0.20682595792852715 chr14 107349540 6255718 0.05827428790100079 0.2989806223862274 chr15 102531392 3111193 0.03034380924039342 0.20069530825087054 chr16 90354753 2697900 0.029858971558474626 0.2527161902795219 chr17 81195210 6006261 0.07397309521091207 0.3710355839887482 chr18 78077248 3609567 0.04623071499651217 0.8288611949219222 chr19 59128983 2132505 0.03606530827699168 0.6941602125822519 chr20 63025520 1871350 0.02969194066149712 0.21908824570703403 chr21 48129895 2343009 0.048680949750669514 0.2701523952396513 chr22 51304566 1593541 0.03106041282953256 0.20419864652705508 chrMT 16571 1030920 62.212298593929155 37.54407379498719 chrX 155270560 7169230 0.046172500440521375 0.30124785980661867 chrY 59373566 283207 0.0047699173062975535 0.11239946081696782