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Triticum dicoccoides vs Hordeum vulgare LastZ Results

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Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Triticum dicoccoides 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: 3,357,299

Genome coverage (bp) Coding exon coverage (bp)
Triticum dicoccoides

Uncovered: 8,832,852,184 out of 10,079,039,394
Covered: 1,246,187,210 out of 10,079,039,394

Uncovered: 2,715,730 out of 81,268,905
Matches: 69,956,824 out of 81,268,905
Mismatches: 7,741,500 out of 81,268,905
Insertions: 854,851 out of 81,268,905

Hordeum vulgare subsp. vulgare

Uncovered: 3,995,118,014 out of 4,834,432,680
Covered: 839,314,666 out of 4,834,432,680

Uncovered: 2,032,746 out of 44,420,163
Matches: 38,005,990 out of 44,420,163
Mismatches: 3,810,576 out of 44,420,163
Insertions: 570,851 out of 44,420,163

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)--hspthresh=5000 --gappedthresh=2200 --inner=2200 --ambiguous=iupac

Chunking parameters

Triticum dicoccoides 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}