Oryza meridionalis vs Oryza longistaminata LastZ Results

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Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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: 304,216

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

Uncovered: 130,998,641 out of 335,668,232
Covered: 204,669,591 out of 335,668,232

Uncovered: 1,628,944 out of 35,224,824
Matches: 31,274,950 out of 35,224,824
Mismatches: 1,869,053 out of 35,224,824
Insertions: 451,877 out of 35,224,824

Oryza longistaminata

Uncovered: 149,025,185 out of 326,442,508
Covered: 177,417,323 out of 326,442,508

Uncovered: 7,610,479 out of 34,512,301
Matches: 25,998,247 out of 34,512,301
Mismatches: 765,180 out of 34,512,301
Insertions: 138,395 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

Oryza meridionalis 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}