Arabidopsis thaliana vs Hordeum vulgare GoldenPromise LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Hordeum vulgare GoldenPromise (Hordeum vulgare subsp. vulgare, GPv1) 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: 150,542

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

Uncovered: 93,472,044 out of 119,667,750
Covered: 26,195,706 out of 119,667,750

Uncovered: 14,332,469 out of 33,775,569
Matches: 12,511,863 out of 33,775,569
Mismatches: 6,537,691 out of 33,775,569
Insertions: 393,546 out of 33,775,569

Hordeum vulgare subsp. vulgare

Uncovered: 4,089,343,249 out of 4,129,363,524
Covered: 40,020,275 out of 4,129,363,524

Uncovered: 27,707,546 out of 49,219,799
Matches: 13,730,577 out of 49,219,799
Mismatches: 7,278,811 out of 49,219,799
Insertions: 502,865 out of 49,219,799

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 GoldenPromise
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options