Vitis vinifera vs Oryza longistaminata LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) 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: 159,489

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

Uncovered: 450,047,473 out of 486,265,422
Covered: 36,217,949 out of 486,265,422

Uncovered: 11,113,719 out of 32,794,161
Matches: 13,762,446 out of 32,794,161
Mismatches: 7,478,280 out of 32,794,161
Insertions: 439,716 out of 32,794,161

Oryza longistaminata

Uncovered: 292,875,989 out of 326,442,508
Covered: 33,566,519 out of 326,442,508

Uncovered: 13,852,890 out of 34,512,301
Matches: 13,533,361 out of 34,512,301
Mismatches: 6,696,082 out of 34,512,301
Insertions: 429,968 out of 34,512,301

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 Oryza longistaminata
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}