Oryza longistaminata vs Oryza nivara LastZ Results

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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) 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: 256,996

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

Uncovered: 89,441,394 out of 326,442,508
Covered: 237,001,114 out of 326,442,508

Uncovered: 904,271 out of 34,512,301
Matches: 32,392,519 out of 34,512,301
Mismatches: 1,048,602 out of 34,512,301
Insertions: 166,909 out of 34,512,301

Oryza sativa f. spontanea

Uncovered: 128,808,237 out of 337,950,324
Covered: 209,142,087 out of 337,950,324

Uncovered: 7,456,510 out of 42,562,444
Matches: 33,780,590 out of 42,562,444
Mismatches: 1,050,053 out of 42,562,444
Insertions: 275,291 out of 42,562,444

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 nivara
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}