Triticum dicoccoides vs Aegilops tauschii LastZ Results

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Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) 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: 3,827,860

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

Uncovered: 7,988,059,492 out of 10,079,039,394
Covered: 2,090,979,902 out of 10,079,039,394

Uncovered: 1,122,760 out of 81,268,905
Matches: 75,635,463 out of 81,268,905
Mismatches: 3,984,775 out of 81,268,905
Insertions: 525,907 out of 81,268,905

Aegilops tauschii subsp. strangulata

Uncovered: 3,163,916,779 out of 4,224,915,394
Covered: 1,060,998,615 out of 4,224,915,394

Uncovered: 864,497 out of 53,210,770
Matches: 49,096,495 out of 53,210,770
Mismatches: 2,815,807 out of 53,210,770
Insertions: 433,971 out of 53,210,770

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 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}