Brachypodium distachyon vs Triticum aestivum LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, v1.0) and Triticum aestivum (Triticum aestivum, IWGSC1+popseq) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. 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: 1,707,392

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

Uncovered: 139,477,066 out of 271,923,306
Covered: 132,446,240 out of 271,923,306

Uncovered: 1,462,332 out of 34,177,820
Matches: 26,749,632 out of 34,177,820
Mismatches: 5,185,764 out of 34,177,820
Insertions: 780,092 out of 34,177,820

Triticum aestivum

Uncovered: 5,698,719,553 out of 6,378,515,436
Covered: 679,795,883 out of 6,378,515,436

Uncovered: 4,021,042 out of 87,732,694
Matches: 70,193,854 out of 87,732,694
Mismatches: 12,328,359 out of 87,732,694
Insertions: 1,189,439 out of 87,732,694

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 20,000,000 50,100,000
Overlap 10,000 10,000
Group set size 0 50,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}