Oryza longistaminata vs Oryza glumipatula LastZ Results

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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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: 298,706

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

Uncovered: 81,425,776 out of 326,442,508
Covered: 245,016,732 out of 326,442,508

Uncovered: 532,955 out of 34,512,301
Matches: 32,665,240 out of 34,512,301
Mismatches: 1,141,760 out of 34,512,301
Insertions: 172,346 out of 34,512,301

Oryza glumipatula

Uncovered: 164,619,036 out of 372,860,283
Covered: 208,241,247 out of 372,860,283

Uncovered: 6,321,983 out of 41,246,944
Matches: 33,588,726 out of 41,246,944
Mismatches: 1,057,384 out of 41,246,944
Insertions: 278,851 out of 41,246,944

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 glumipatula
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}