BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819008.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 = 891,485 number of mapped reads = 874,853 (98.13%) number of supplementary alignments = 13,849 (1.55%) number of secondary alignments = 0 number of mapped bases = 80,749,258 bp number of sequenced bases = 80,698,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,233 duplication rate = 30.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0524 >>>>>>> ACTG content number of A's = 23,656,367 bp (29.31%) number of C's = 17,451,140 bp (21.63%) number of T's = 22,839,744 bp (28.3%) number of G's = 16,746,846 bp (20.75%) number of N's = 4,252 bp (0.01%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 553,307 number of insertions = 14,375 mapped reads with insertion percentage = 1.59% number of deletions = 26,992 mapped reads with deletion percentage = 3.02% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.3923X There is a 1.49% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 8276989 0.03320749600058168 0.696226810785362 chr2 243199373 6720602 0.027634125520545647 0.585060881071737 chr3 198022430 4166715 0.0210416314959876 0.22656420726828025 chr4 191154276 4517970 0.02363520238490506 0.2801588352810373 chr5 180915260 4331373 0.02394144639871728 0.2512556447144441 chr6 171115067 3295890 0.019261249507619337 0.25075825981118377 chr7 159138663 4053062 0.02546874482664216 0.3912215766931221 chr8 146364022 7293123 0.04982865939554462 0.37602994809783313 chr9 141213431 3436030 0.024332175598792725 0.33554729573423925 chr10 135534747 4363019 0.03219114726351317 0.49551261635499855 chr11 135006516 2605886 0.019301927619552822 0.2495213389447165 chr12 133851895 3647091 0.027247212301327522 0.264035965830744 chr13 115169878 1748713 0.015183770534166929 0.19108814726021534 chr14 107349540 1865735 0.01737999995156011 0.2184950748594177 chr15 102531392 2110832 0.02058717782745015 0.22429060003574702 chr16 90354753 2684476 0.029710401621041452 0.466475913917937 chr17 81195210 2854274 0.03515323132977918 0.3198533349166107 chr18 78077248 1912637 0.024496726626430276 0.3963817855532562 chr19 59128983 1671436 0.028267626385524 0.5523893568972436 chr20 63025520 2262742 0.035901996524582425 0.3168776641846522 chr21 48129895 1148693 0.023866517888725916 0.2728627668713394 chr22 51304566 652577 0.012719667095517386 0.19062936457315066 chrMT 16571 47185 2.847444330456822 3.2738733633337067 chrX 155270560 4730349 0.03046520216066716 0.32841924689007107 chrY 59373566 351859 0.005926189442621654 0.4336678216320374