BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926930.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 10,245,610 number of mapped reads = 9,960,504 (97.22%) number of supplementary alignments = 362,091 (3.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,999,921 number of mapped paired reads (second in pair) = 4,960,583 number of mapped paired reads (both in pair) = 9,801,212 number of mapped paired reads (singletons) = 159,292 number of mapped bases = 904,935,222 bp number of sequenced bases = 904,213,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 587,841 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 387,126.4782 std insert size = 6,085,609.2778 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 52.4446 >>>>>>> ACTG content number of A's = 257,864,239 bp (28.52%) number of C's = 176,057,508 bp (19.47%) number of T's = 262,693,850 bp (29.05%) number of G's = 207,421,410 bp (22.94%) number of N's = 176,245 bp (0.02%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 8,639,755 number of insertions = 160,754 mapped reads with insertion percentage = 1.58% number of deletions = 486,604 mapped reads with deletion percentage = 4.76% homopolymer indels = 51.64% >>>>>>> Coverage mean coverageData = 0.2923X std coverageData = 1.3205X There is a 17.82% of reference with a coverageData >= 1X There is a 6.58% of reference with a coverageData >= 2X There is a 2.41% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 75590281 0.30327018122053145 1.2491022355560895 chr2 243199373 76468947 0.31442904665712273 2.2234220487898084 chr3 198022430 63057143 0.3184343460485764 0.813295043536991 chr4 191154276 54914887 0.28728045298866345 1.2979896970521176 chr5 180915260 55622015 0.3074478902443055 0.7896539781713157 chr6 171115067 54058966 0.3159217183370533 1.4369117946386751 chr7 159138663 47659152 0.2994819178542426 1.0112871017821823 chr8 146364022 47925745 0.32744211552207825 0.8796500431877913 chr9 141213431 40821340 0.28907547753017915 1.409565773227561 chr10 135534747 45479333 0.33555478581444503 2.787914230727953 chr11 135006516 43035797 0.3187682955984139 0.9917064955082704 chr12 133851895 39578740 0.2956905466299151 0.8111585537645248 chr13 115169878 28193078 0.24479558795746922 0.7002971643893716 chr14 107349540 27492721 0.2561046931360861 0.7400111889523778 chr15 102531392 26076314 0.2543251729187486 0.727941084806553 chr16 90354753 26425152 0.2924600103770966 1.7508016686849404 chr17 81195210 22160345 0.2729267526988353 0.8730670721877181 chr18 78077248 23533484 0.30141282643568584 1.3378699875135263 chr19 59128983 14433421 0.24410061306144906 0.9406759217002254 chr20 63025520 18539268 0.2941549391421126 0.8289632569007829 chr21 48129895 10031235 0.20842004745699114 1.0060615856592807 chr22 51304566 10971078 0.21384213638996577 0.7125355709249126 chrMT 16571 54462 3.2865849978878763 3.22483724402169 chrX 155270560 50999781 0.3284575066902573 0.8733981689956752 chrY 59373566 1812537 0.030527676238951185 1.3763342985235407