Brachypodium distachyon vs Triticum aestivum LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, v1.0) and Triticum aestivum (Triticum aestivum, TGACv1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 85. Brachypodium distachyon 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: 723,900

Genome coverage (bp) Coding exon coverage (bp)
Brachypodium distachyon

Uncovered: 159,603,325 out of 271,923,306
Covered: 112,319,981 out of 271,923,306

Uncovered: 2,120,098 out of 34,177,820
Matches: 26,295,560 out of 34,177,820
Mismatches: 5,036,278 out of 34,177,820
Insertions: 725,884 out of 34,177,820

Triticum aestivum

Uncovered: 4,127,930,846 out of 4,386,473,599
Covered: 258,542,753 out of 4,386,473,599

Uncovered: 3,601,853 out of 41,298,743
Matches: 30,311,963 out of 41,298,743
Mismatches: 6,521,481 out of 41,298,743
Insertions: 863,446 out of 41,298,743

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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

Brachypodium distachyon Triticum aestivum
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}