Oryza longistaminata vs Oryza sativa Japonica Group LastZ Results

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Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) 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: 350,224

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

Uncovered: 63,545,502 out of 326,442,508
Covered: 262,897,006 out of 326,442,508

Uncovered: 941,072 out of 34,512,301
Matches: 32,369,355 out of 34,512,301
Mismatches: 1,041,484 out of 34,512,301
Insertions: 160,390 out of 34,512,301

Oryza sativa Japonica Group

Uncovered: 162,259,490 out of 375,049,285
Covered: 212,789,795 out of 375,049,285

Uncovered: 5,793,168 out of 34,403,043
Matches: 27,643,372 out of 34,403,043
Mismatches: 772,319 out of 34,403,043
Insertions: 194,184 out of 34,403,043

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 sativa Japonica Group
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}