Brachypodium distachyon vs Hordeum vulgare LastZ Results

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Brachypodium distachyon (Brachypodium distachyon, v1.0) and Hordeum vulgare (Hordeum vulgare, Hv_IBSC_PGSB_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: 768,709

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

Uncovered: 164,829,349 out of 271,923,306
Covered: 107,093,957 out of 271,923,306

Uncovered: 2,140,317 out of 34,177,820
Matches: 26,251,309 out of 34,177,820
Mismatches: 5,075,621 out of 34,177,820
Insertions: 710,573 out of 34,177,820

Hordeum vulgare

Uncovered: 4,546,678,235 out of 4,833,907,081
Covered: 287,228,846 out of 4,833,907,081

Uncovered: 4,086,888 out of 44,392,268
Matches: 32,601,817 out of 44,392,268
Mismatches: 6,695,956 out of 44,392,268
Insertions: 1,007,607 out of 44,392,268

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}