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Oryza glumipatula vs Oryza rufipogon LastZ results

Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza glumipatula 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 glumipatulaOryza rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 146,436 alignment blocks

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

Uncovered: 113,576,679 out of 372,860,283
Covered: 259,283,604 out of 372,860,283

Uncovered: 306,007 out of 41,162,840
Matches: 39,896,681 out of 41,162,840
Mismatches: 778,336 out of 41,162,840
Insertions: 181,816 out of 41,162,840
Identity over aligned base-pairs: 97.6%

Oryza rufipogon

Uncovered: 92,964,917 out of 338,040,714
Covered: 245,075,797 out of 338,040,714

Uncovered: 3,368,235 out of 42,764,129
Matches: 38,713,170 out of 42,764,129
Mismatches: 545,110 out of 42,764,129
Insertions: 137,614 out of 42,764,129
Identity over aligned base-pairs: 98.3%