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Oryza nivara vs Oryza rufipogon LastZ results

Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza nivara 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 nivaraOryza rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 113,440 alignment blocks

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

Uncovered: 61,727,093 out of 337,950,324
Covered: 276,223,231 out of 337,950,324

Uncovered: 235,524 out of 42,480,949
Matches: 41,486,776 out of 42,480,949
Mismatches: 619,930 out of 42,480,949
Insertions: 138,719 out of 42,480,949
Identity over aligned base-pairs: 98.2%

Oryza rufipogon

Uncovered: 73,293,586 out of 338,040,714
Covered: 264,747,128 out of 338,040,714

Uncovered: 2,229,427 out of 42,764,129
Matches: 40,081,271 out of 42,764,129
Mismatches: 358,472 out of 42,764,129
Insertions: 94,959 out of 42,764,129
Identity over aligned base-pairs: 98.9%