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Oryza meridionalis vs Oryza longistaminata LastZ results

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 80. Oryza meridionalis was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza meridionalisOryza longistaminata
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 304,216 alignment blocks

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
Identity over aligned base-pairs: 93.1%

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
Identity over aligned base-pairs: 96.6%