Arabidopsis thaliana vs Oryza longistaminata LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. 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: 80,763

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

Uncovered: 93,513,658 out of 119,667,750
Covered: 26,154,092 out of 119,667,750

Uncovered: 13,993,484 out of 33,462,323
Matches: 12,727,695 out of 33,462,323
Mismatches: 6,377,717 out of 33,462,323
Insertions: 363,427 out of 33,462,323

Oryza longistaminata

Uncovered: 308,172,523 out of 326,442,508
Covered: 18,269,985 out of 326,442,508

Uncovered: 22,749,820 out of 34,512,301
Matches: 7,660,379 out of 34,512,301
Mismatches: 3,826,340 out of 34,512,301
Insertions: 275,762 out of 34,512,301

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Arabidopsis thaliana Oryza longistaminata
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}