Arabidopsis thaliana vs Oryza brachyantha LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Arabidopsis thaliana 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: 78,436

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,841,766 out of 119,667,750
Covered: 25,825,984 out of 119,667,750

Uncovered: 14,162,601 out of 33,462,323
Matches: 12,630,962 out of 33,462,323
Mismatches: 6,314,345 out of 33,462,323
Insertions: 354,415 out of 33,462,323

Oryza brachyantha

Uncovered: 242,764,829 out of 260,838,168
Covered: 18,073,339 out of 260,838,168

Uncovered: 21,003,634 out of 33,473,466
Matches: 8,131,384 out of 33,473,466
Mismatches: 4,059,111 out of 33,473,466
Insertions: 279,337 out of 33,473,466

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)