Vitis vinifera vs Eragrostis curvula LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Eragrostis curvula (Eragrostis curvula, CERZOS_E.curvula1.0) 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: 214,780

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

Uncovered: 449,904,623 out of 486,265,422
Covered: 36,360,799 out of 486,265,422

Uncovered: 10,486,925 out of 32,794,161
Matches: 14,532,049 out of 32,794,161
Mismatches: 7,275,652 out of 32,794,161
Insertions: 499,535 out of 32,794,161

Eragrostis curvula

Uncovered: 551,398,286 out of 603,072,269
Covered: 51,673,983 out of 603,072,269

Uncovered: 30,953,363 out of 62,628,176
Matches: 20,535,505 out of 62,628,176
Mismatches: 10,417,499 out of 62,628,176
Insertions: 721,809 out of 62,628,176

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 Eragrostis curvula
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options