Vitis vinifera vs Hordeum vulgare LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) 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: 250,538

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

Uncovered: 446,621,355 out of 486,265,422
Covered: 39,644,067 out of 486,265,422

Uncovered: 10,585,218 out of 32,794,161
Matches: 14,266,418 out of 32,794,161
Mismatches: 7,478,435 out of 32,794,161
Insertions: 464,090 out of 32,794,161

Hordeum vulgare subsp. vulgare

Uncovered: 4,773,954,905 out of 4,834,432,680
Covered: 60,477,775 out of 4,834,432,680

Uncovered: 18,218,495 out of 44,420,163
Matches: 16,876,048 out of 44,420,163
Mismatches: 8,673,243 out of 44,420,163
Insertions: 652,377 out of 44,420,163

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 Hordeum vulgare
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}