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Arabidopsis thaliana vs Hordeum vulgare LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 165,915

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 92,861,049 out of 119,667,750
Covered: 26,806,701 out of 119,667,750

Uncovered: 14,177,475 out of 33,775,569
Matches: 12,474,087 out of 33,775,569
Mismatches: 6,731,462 out of 33,775,569
Insertions: 392,545 out of 33,775,569

Hordeum vulgare subsp. vulgare

Uncovered: 4,788,489,275 out of 4,834,432,680
Covered: 45,943,405 out of 4,834,432,680

Uncovered: 21,702,856 out of 44,420,163
Matches: 14,435,720 out of 44,420,163
Mismatches: 7,665,119 out of 44,420,163
Insertions: 616,468 out of 44,420,163

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
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

Chunking parameters

Arabidopsis thaliana 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}