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Oryza meridionalis vs Oryza rufipogon LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza rufipogon (Oryza rufipogon, OR_W1943) 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 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 rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 230,844 alignment blocks

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

Uncovered: 129,422,977 out of 335,668,232
Covered: 206,245,255 out of 335,668,232

Uncovered: 537,574 out of 35,224,824
Matches: 33,436,555 out of 35,224,824
Mismatches: 998,009 out of 35,224,824
Insertions: 252,686 out of 35,224,824
Identity over aligned base-pairs: 96.4%

Oryza rufipogon

Uncovered: 150,081,714 out of 338,040,714
Covered: 187,959,000 out of 338,040,714

Uncovered: 8,048,799 out of 42,763,723
Matches: 33,641,273 out of 42,763,723
Mismatches: 834,626 out of 42,763,723
Insertions: 239,025 out of 42,763,723
Identity over aligned base-pairs: 96.9%