Brachypodium distachyon vs Hordeum vulgare LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 762,152

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

Uncovered: 159,459,943 out of 271,163,419
Covered: 111,703,476 out of 271,163,419

Uncovered: 3,481,517 out of 39,007,317
Matches: 28,122,124 out of 39,007,317
Mismatches: 6,570,672 out of 39,007,317
Insertions: 833,004 out of 39,007,317

Hordeum vulgare subsp. vulgare

Uncovered: 4,537,536,077 out of 4,834,432,680
Covered: 296,896,603 out of 4,834,432,680

Uncovered: 3,657,309 out of 44,420,163
Matches: 32,728,807 out of 44,420,163
Mismatches: 7,016,701 out of 44,420,163
Insertions: 1,017,346 out of 44,420,163

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 Hordeum vulgare
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}