Triticum dicoccoides vs Triticum aestivum LastZ Results

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Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Triticum aestivum (Triticum aestivum, IWGSC) 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: 1,497,407

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

Uncovered: 2,434,228,557 out of 10,079,039,394
Covered: 7,644,810,837 out of 10,079,039,394

Uncovered: 12,403,620 out of 81,268,905
Matches: 67,719,060 out of 81,268,905
Mismatches: 1,025,922 out of 81,268,905
Insertions: 120,303 out of 81,268,905

Triticum aestivum

Uncovered: 6,896,989,580 out of 14,547,261,565
Covered: 7,650,271,985 out of 14,547,261,565

Uncovered: 58,841,815 out of 133,674,966
Matches: 73,354,621 out of 133,674,966
Mismatches: 1,337,166 out of 133,674,966
Insertions: 141,364 out of 133,674,966

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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 --identity=75..100

Chunking parameters

Triticum dicoccoides Triticum aestivum
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options