Oryza longistaminata vs Oryza rufipogon LastZ Results

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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza longistaminata 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: 263,364

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 87,603,496 out of 326,442,508
Covered: 238,839,012 out of 326,442,508

Uncovered: 868,270 out of 34,512,301
Matches: 32,455,574 out of 34,512,301
Mismatches: 1,027,417 out of 34,512,301
Insertions: 161,040 out of 34,512,301

Oryza rufipogon

Uncovered: 126,670,012 out of 338,040,714
Covered: 211,370,702 out of 338,040,714

Uncovered: 7,551,780 out of 42,763,723
Matches: 33,903,612 out of 42,763,723
Mismatches: 1,036,850 out of 42,763,723
Insertions: 271,481 out of 42,763,723

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

Oryza longistaminata Oryza rufipogon
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}