BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085129.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 = 1,885,669 number of mapped reads = 1,670,388 (88.58%) number of supplementary alignments = 12,863 (0.68%) number of secondary alignments = 0 number of mapped bases = 111,089,047 bp number of sequenced bases = 111,050,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,378 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.421 >>>>>>> ACTG content number of A's = 30,770,563 bp (27.71%) number of C's = 20,705,009 bp (18.64%) number of T's = 34,640,425 bp (31.19%) number of G's = 24,909,427 bp (22.43%) number of N's = 24,882 bp (0.02%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 968,463 number of insertions = 8,725 mapped reads with insertion percentage = 0.52% number of deletions = 24,251 mapped reads with deletion percentage = 1.44% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.3176X There is a 3.21% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.03% 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 8779052 0.03522178586668396 0.5281121440887462 chr2 243199373 9503019 0.03907501439158727 0.41596178782959425 chr3 198022430 7621311 0.03848710976832271 0.21213821105437491 chr4 191154276 7453812 0.03899369742584257 0.22041249641759347 chr5 180915260 6939804 0.038359417552726066 0.2137932039517316 chr6 171115067 6587239 0.03849596131707093 0.24765867983535678 chr7 159138663 6238907 0.039204219027528214 0.42812787905048905 chr8 146364022 5707183 0.03899307303812682 0.43677594324324776 chr9 141213431 4696292 0.03325669496692563 0.2967347480859984 chr10 135534747 5136750 0.037899875225354575 0.2874393207566824 chr11 135006516 5106267 0.03782237444006036 0.28252712233707006 chr12 133851895 5106700 0.0381518692731246 0.21577027094521647 chr13 115169878 3691081 0.032049013718673906 0.1958580321211765 chr14 107349540 3405446 0.0317229677928755 0.20484985210477502 chr15 102531392 3134143 0.0305676431272873 0.1955551668367675 chr16 90354753 2997653 0.03317648380932434 0.21558120785735246 chr17 81195210 2839521 0.034971533419274364 0.22139651930617102 chr18 78077248 2997115 0.03838653483278509 0.5063075595043088 chr19 59128983 2085953 0.035278012476554856 0.40481524835746663 chr20 63025520 2229691 0.03537758990326458 0.20808027863048387 chr21 48129895 869279 0.018061103187530327 0.1565874770010408 chr22 51304566 1157023 0.022552047316802173 0.1614720937883319 chrMT 16571 4649 0.2805503590610102 0.6058413820340026 chrX 155270560 6535752 0.04209266714823467 0.24497688298121492 chrY 59373566 265405 0.004470086907025258 0.09814659846591477