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Oryza rufipogon vs Oryza brachyantha LastZ results

Oryza rufipogon (Oryza rufipogon, OR_W1943) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza rufipogon 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 rufipogonOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 271,668 alignment blocks

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

Uncovered: 205,609,686 out of 338,040,714
Covered: 132,431,028 out of 338,040,714

Uncovered: 5,331,463 out of 42,764,129
Matches: 31,739,235 out of 42,764,129
Mismatches: 4,816,999 out of 42,764,129
Insertions: 876,432 out of 42,764,129
Identity over aligned base-pairs: 84.8%

Oryza brachyantha

Uncovered: 142,748,506 out of 250,927,218
Covered: 108,178,712 out of 250,927,218

Uncovered: 2,272,575 out of 30,210,943
Matches: 24,773,121 out of 30,210,943
Mismatches: 2,738,870 out of 30,210,943
Insertions: 426,377 out of 30,210,943
Identity over aligned base-pairs: 88.7%