BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926961.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 = 15,290,832 number of mapped reads = 14,907,392 (97.49%) number of supplementary alignments = 555,156 (3.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,445,159 number of mapped paired reads (second in pair) = 7,462,233 number of mapped paired reads (both in pair) = 14,682,858 number of mapped paired reads (singletons) = 224,534 number of mapped bases = 1,357,071,369 bp number of sequenced bases = 1,356,024,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,129,950 duplication rate = 6.06% >>>>>>> Insert size mean insert size = 383,475.3183 std insert size = 6,072,523.4457 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 52.6695 >>>>>>> ACTG content number of A's = 383,423,118 bp (28.28%) number of C's = 268,405,139 bp (19.79%) number of T's = 389,970,419 bp (28.76%) number of G's = 314,169,091 bp (23.17%) number of N's = 57,066 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 12,938,351 number of insertions = 239,046 mapped reads with insertion percentage = 1.58% number of deletions = 700,871 mapped reads with deletion percentage = 4.58% homopolymer indels = 51.94% >>>>>>> Coverage mean coverageData = 0.4384X std coverageData = 1.7737X There is a 22.32% of reference with a coverageData >= 1X There is a 9.96% of reference with a coverageData >= 2X There is a 4.72% of reference with a coverageData >= 3X There is a 2.49% of reference with a coverageData >= 4X There is a 1.38% of reference with a coverageData >= 5X There is a 0.81% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 113665706 0.45602978056371624 2.0641713723103265 chr2 243199373 110592503 0.45474008273861793 2.5134825794331115 chr3 198022430 84189959 0.4251536505233271 1.0798012968485304 chr4 191154276 72256217 0.37799948037782843 1.562973473436477 chr5 180915260 73645158 0.4070699066513239 1.0322744280870149 chr6 171115067 72501268 0.4236989136672576 1.1139989339341472 chr7 159138663 65512014 0.41166623349097764 1.1500657503880087 chr8 146364022 61517968 0.42030799071646174 1.110629831579372 chr9 141213431 54345547 0.38484687055015326 1.5094399690153317 chr10 135534747 61975497 0.4572664823729667 3.0721686775502395 chr11 135006516 62720307 0.46457244330340325 1.3648003421155288 chr12 133851895 58446910 0.43665358641355057 1.1357713158597171 chr13 115169878 67652948 0.5874187693417544 1.381921564164415 chr14 107349540 39137463 0.3645796991770994 1.0061595232320786 chr15 102531392 40289396 0.3929469327793775 1.0670246969484658 chr16 90354753 74774175 0.8275621648813538 2.032929600550589 chr17 81195210 41832269 0.5152061186860654 1.3224718235697184 chr18 78077248 30900231 0.39576485841304243 1.6230831358951867 chr19 59128983 29703873 0.5023572450079177 1.658064357302906 chr20 63025520 34045084 0.5401793432247762 1.3799130196527687 chr21 48129895 16305991 0.3387913270951453 1.7042886888147077 chr22 51304566 19793234 0.38579868310356624 1.0996651265371247 chrMT 16571 3540269 213.64244764950817 236.3669716277019 chrX 155270560 64811509 0.4174101581136823 1.0828032862001968 chrY 59373566 2915873 0.04911062609916339 1.1683632956789836