Zea mays vs Brachypodium distachyon LastZ Results

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Zea mays (Zea mays, AGPv4) and Brachypodium distachyon (Brachypodium distachyon, v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 81. Zea mays 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: 236,216

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,026,934,362 out of 2,134,373,047
Covered: 107,438,685 out of 2,134,373,047

Uncovered: 5,177,825 out of 48,311,124
Matches: 33,318,301 out of 48,311,124
Mismatches: 8,676,214 out of 48,311,124
Insertions: 1,138,784 out of 48,311,124

Brachypodium distachyon

Uncovered: 219,453,070 out of 271,923,306
Covered: 52,470,236 out of 271,923,306

Uncovered: 8,805,557 out of 34,177,820
Matches: 19,996,627 out of 34,177,820
Mismatches: 4,801,234 out of 34,177,820
Insertions: 574,402 out of 34,177,820

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

Zea mays 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}