Oryza barthii vs Oryza glaberrima LastZ Results

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Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza glaberrima (Oryza glaberrima, AGI1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza barthii was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.


Number of alignment blocks: 113,186

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

Uncovered: 45,335,588 out of 308,272,304
Covered: 262,936,716 out of 308,272,304

Uncovered: 3,956,501 out of 39,538,509
Matches: 29,650,119 out of 39,538,509
Mismatches: 5,763,874 out of 39,538,509
Insertions: 168,015 out of 39,538,509

Oryza glaberrima

Uncovered: 77,325,763 out of 316,419,574
Covered: 239,093,811 out of 316,419,574

Uncovered: 7,170,035 out of 36,293,721
Matches: 24,893,257 out of 36,293,721
Mismatches: 4,151,987 out of 36,293,721
Insertions: 78,442 out of 36,293,721

Configuration parameters

Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)