Vitis vinifera vs Actinidia chinensis LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Actinidia chinensis (Actinidia chinensis var. chinensis, Red5_PS1_1.69.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 203,863

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 409,905,082 out of 486,265,422
Covered: 76,360,340 out of 486,265,422

Uncovered: 3,409,843 out of 32,794,161
Matches: 21,331,007 out of 32,794,161
Mismatches: 7,505,970 out of 32,794,161
Insertions: 547,341 out of 32,794,161

Actinidia chinensis var. chinensis

Uncovered: 502,919,506 out of 553,842,477
Covered: 50,922,971 out of 553,842,477

Uncovered: 19,673,455 out of 42,227,027
Matches: 16,652,083 out of 42,227,027
Mismatches: 5,519,667 out of 42,227,027
Insertions: 381,822 out of 42,227,027

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Vitis vinifera Actinidia chinensis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}