Hordeum vulgare vs Aegilops tauschii LastZ Results

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Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 2,216,922

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

Uncovered: 3,999,755,092 out of 4,834,432,680
Covered: 834,677,588 out of 4,834,432,680

Uncovered: 2,265,301 out of 44,420,163
Matches: 37,854,235 out of 44,420,163
Mismatches: 3,745,134 out of 44,420,163
Insertions: 555,493 out of 44,420,163

Aegilops tauschii subsp. strangulata

Uncovered: 3,586,080,388 out of 4,224,915,394
Covered: 638,835,006 out of 4,224,915,394

Uncovered: 2,608,677 out of 53,210,770
Matches: 43,999,234 out of 53,210,770
Mismatches: 5,872,244 out of 53,210,770
Insertions: 730,615 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

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}