Hordeum vulgare vs Brachypodium distachyon LastZ Results

Back to all analyses

Hordeum vulgare (Hordeum vulgare, ASM32608v1) and Brachypodium distachyon (Brachypodium distachyon, v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Hordeum vulgare 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: 556,079

Genome coverage (bp) Coding exon coverage (bp)
Hordeum vulgare

Uncovered: 3,847,651,646 out of 4,045,300,851
Covered: 197,649,205 out of 4,045,300,851

Uncovered: 1,245,127 out of 27,753,036
Matches: 21,918,391 out of 27,753,036
Mismatches: 4,090,959 out of 27,753,036
Insertions: 498,559 out of 27,753,036

Brachypodium distachyon

Uncovered: 157,018,706 out of 271,923,306
Covered: 114,904,600 out of 271,923,306

Uncovered: 1,823,289 out of 34,177,820
Matches: 26,571,776 out of 34,177,820
Mismatches: 5,078,607 out of 34,177,820
Insertions: 704,148 out of 34,177,820

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

Hordeum vulgare Brachypodium distachyon
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}