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Triticum aestivum vs Aegilops tauschii LastZ Results

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Triticum aestivum (Triticum aestivum, IWGSC) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Triticum aestivum 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.


Number of alignment blocks: 3,367,129

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

Uncovered: 9,459,434,471 out of 14,547,261,565
Covered: 5,087,827,094 out of 14,547,261,565

Uncovered: 2,219,839 out of 133,674,966
Matches: 125,566,624 out of 133,674,966
Mismatches: 5,336,728 out of 133,674,966
Insertions: 551,775 out of 133,674,966

Aegilops tauschii subsp. strangulata

Uncovered: 1,049,682,512 out of 4,224,915,394
Covered: 3,175,232,882 out of 4,224,915,394

Uncovered: 276,949 out of 53,210,770
Matches: 52,165,082 out of 53,210,770
Mismatches: 671,604 out of 53,210,770
Insertions: 97,135 out of 53,210,770

Configuration parameters

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)
     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 aestivum 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}