Hordeum vulgare vs Aegilops tauschii LastZ Results

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Hordeum vulgare (Hordeum vulgare, ASM32608v1) and Aegilops tauschii (Aegilops tauschii, ASM34733v1) 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: 4,131,535

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

Uncovered: 3,181,229,528 out of 4,045,300,851
Covered: 864,071,323 out of 4,045,300,851

Uncovered: 673,272 out of 27,753,036
Matches: 24,615,669 out of 27,753,036
Mismatches: 2,148,729 out of 27,753,036
Insertions: 315,366 out of 27,753,036

Aegilops tauschii

Uncovered: 2,324,359,223 out of 3,313,764,331
Covered: 989,405,108 out of 3,313,764,331

Uncovered: 1,627,638 out of 40,847,881
Matches: 34,499,986 out of 40,847,881
Mismatches: 4,179,480 out of 40,847,881
Insertions: 540,777 out of 40,847,881

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 Aegilops tauschii
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}