UC Davis UC Davis - Viticulture and Enology

Vitis vinifera cv. Carménère

Cantu Lab

Citation

Diploid Genome Assembly of the Wine Grape Carménère
Andrea Minio, Mélanie Massonnet, Rosa Figueroa-Balderas, Alvaro Castro and Dario Cantu
G3: GENES, GENOMES, GENETICS Early online March 28, 2019; https://doi.org/10.1534/g3.119.400030

Primary and Haplotigs Statisitcs

Genome Assembly

Genome length:           1,043,140,749
Number of sequences:             9,380
Average sequence length:       111,209.04
Median seqence length           33,992
Minimum sequence length:           507
Maximum sequence length:     5,905,621
N25 length: 1,235,567      Index:    124
N50 length:   412,996      Index:    507
N75 length:   113,579      Index:  1,729
N90 length:    37,096      Index:  4,317
Sequences > 500b - Count:       9,380    Cumulative length: 1,043,140,749
Sequences > 1Kb - Count:        9,359    Cumulative length: 1,043,124,834
Sequences > 5Kb - Count:        9,164    Cumulative length: 1,042,503,057
Sequences > 10Kb - Count:       8,686    Cumulative length: 1,038,770,452
Sequences > 50Kb - Count:       3,292    Cumulative length:   895,146,319
Sequences > 100Kb - Count:      1,872    Cumulative length:   797,707,166
Sequences > 500Kb - Count:        402    Cumulative length:   474,122,780
Sequences > 1Mb - Count:          174    Cumulative length:   317,843,538
Sequences > 5Mb - Count:            3    Cumulative length:    17,025,791

Annotation

                           Num of Feat Cumulative Length     Max  Average    St Dev
Loci lengths                    73,109       256,934,202 142,812 3,514.40  5,776.10
mRNAs lengths                   73,109       256,934,202 142,812 3,514.40  5,776.10
Intergenic regions lengths      66,050       569,801,844 321,943 8,626.83 13,794.94
Exons lengths                  296,164        71,515,983   7,992   241.47    328.69
Exons count/mRNA                                              60     4.05      4.17
Introns lengths                223,055       185,418,219 141,659   831.27  1,780.96
CDSs exons lengths             296,164        71,515,983   7,992   241.47    328.69
CDSs exons count/mRNA                                         60     4.05      4.17
mRNAs sequences lengths         73,109        71,515,983  14,328   978.21    786.56
CDSs sequences lengths          73,109        71,515,936  14,328   978.21    786.56
Protein sequences lengths       73,109        23,837,875   4,776   326.06    262.19

Primary Assembly Statisitcs

Genome Assembly

Genome length:	       622,795,289
Number of sequences:	     1,411
Average sequence length:   441,385.75
Median seqence length	   193,714
Minimum sequence length:    20,364
Maximum sequence length: 5,905,621
N25 length:	1,877,721	Index:	55
N50 length:	1,039,379	Index:	168
N75 length:	  451,240	Index:	397
N90 length:	  202,939	Index:	696
Sequences > 100b - Count:	1,411	Cumulative length:	622,795,289
Sequences > 500b - Count:	1,411	Cumulative length:	622,795,289
Sequences > 1Kb - Count:	1,411	Cumulative length:	622,795,289
Sequences > 5Kb - Count:	1,411	Cumulative length:	622,795,289
Sequences > 10Kb - Count:	1,411	Cumulative length:	622,795,289
Sequences > 50Kb - Count:	1,201	Cumulative length:	615,783,550
Sequences > 100Kb - Count:	  947	Cumulative length:	597,265,472
Sequences > 500Kb - Count:	  369	Cumulative length:	454,212,928
Sequences > 1Mb - Count:	  174	Cumulative length:	317,843,538
Sequences > 5Mb - Count:	    3	Cumulative length:	 17,025,791

Annotation

                           Num of Feat Cumulative Length     Max   Average    St Dev
Loci lengths                    40,684       153,833,011 142,812  3,781.17  6,333.65
mRNAs lengths                   40,684       153,833,011 142,812  3,781.17  6,333.65
Intergenic regions lengths      39,351       405,613,626 321,943 10,307.58 16,008.43
Exons lengths                  168,416        42,123,229   7,992    250.11    348.29
Exons count/mRNA                                              60      4.14      4.36
Introns lengths                127,732       111,709,782 141,659    874.56  1,920.38
CDSs exons lengths             168,416        42,123,229   7,992    250.11    348.29
CDSs exons count/mRNA                                         60      4.14      4.36
mRNAs sequences lengths         40,684        42,123,229  14,328  1,035.38    827.88
CDSs sequences lengths          40,684        42,123,214  14,328  1,035.38    827.88
Protein sequences lengths       40,684        14,040,845   4,776    345.12    275.96

Haplotigs Statisitcs

Genome Assembly

Genome length:	         420,345,460
Number of sequences:	       7,969
Average sequence length:      52,747.58
Median seqence lengthi:	      29,398
Minimum sequence length:         507
Maximum sequence length:     743,383
N25 length:	231,329		Index:	  295
N50 length:	 89,565		Index:	1,029
N75 length:	 38,272		Index:	2,921
N90 length:	 23,191		Index:	5,025
Sequences > 500b - Count:  7,969	Cumulative length:	420,345,460
Sequences > 1Kb - Count:   7,948	Cumulative length:	420,329,545
Sequences > 5Kb - Count:   7,753	Cumulative length:	419,707,768
Sequences > 10Kb - Count:  7,275	Cumulative length:	415,975,163
Sequences > 50Kb - Count:  2,091	Cumulative length:	279,362,769
Sequences > 100Kb - Count:   925	Cumulative length:	200,441,694
Sequences > 500Kb - Count:    33	Cumulative length:	 19,909,852
Sequences > 1Mb - Count:       0	Cumulative length:	          0
Sequences > 5Mb - Count:       0	Cumulative length:	          0

Annotation

                           Num of Feat Cumulative Length     Max  Average   St Dev
Loci lengths                    32,425       103,101,191  97,147 3,179.68 4,968.94
mRNAs lengths                   32,425       103,101,191  97,147 3,179.68 4,968.94
Intergenic regions lengths      26,699       164,188,218 204,635 6,149.60 9,097.77
Exons lengths                  127,748        29,392,754   7,992   230.08   300.52
Exons count/mRNA                                              51     3.94     3.93
Introns lengths                 95,323        73,708,437  68,392   773.25 1,573.04
CDSs exons lengths             127,748        29,392,754   7,992   230.08   300.52
CDSs exons count/mRNA                                         51     3.94     3.93
mRNAs sequences lengths         32,425        29,392,754  11,352   906.48   725.07
CDSs sequences lengths          32,425        29,392,722  11,352   906.48   725.07
Protein sequences lengths       32,425         9,797,030   3,784   302.14   241.70

Cantu Lab     |     Webmaster: Dr. Andrea Minio (aminio[at]ucdavis.edu).