Oryza sativa Japonica Group vs Brachypodium distachyon LastZ Results

Back to all analyses

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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.

Results

Number of alignment blocks: 175,305

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 294,783,826 out of 375,049,285
Covered: 80,265,459 out of 375,049,285

Uncovered: 3,560,443 out of 34,403,043
Matches: 24,107,053 out of 34,403,043
Mismatches: 5,921,149 out of 34,403,043
Insertions: 814,398 out of 34,403,043

Brachypodium distachyon

Uncovered: 194,458,588 out of 271,163,419
Covered: 76,704,831 out of 271,163,419

Uncovered: 4,894,871 out of 39,007,317
Matches: 26,768,657 out of 39,007,317
Mismatches: 6,518,372 out of 39,007,317
Insertions: 825,417 out of 39,007,317

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Group Brachypodium distachyon
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}