Hordeum vulgare GoldenPromise vs Triticum aestivum LastZ Results

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Hordeum vulgare GoldenPromise (Hordeum vulgare subsp. vulgare, GPv1) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Hordeum vulgare GoldenPromise 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: 3,208,694

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

Uncovered: 3,420,904,238 out of 4,129,363,524
Covered: 708,459,286 out of 4,129,363,524

Uncovered: 6,307,413 out of 49,219,799
Matches: 38,919,082 out of 49,219,799
Mismatches: 3,534,251 out of 49,219,799
Insertions: 459,053 out of 49,219,799

Triticum aestivum

Uncovered: 13,416,976,482 out of 14,547,261,565
Covered: 1,130,285,083 out of 14,547,261,565

Uncovered: 17,478,254 out of 133,674,966
Matches: 105,973,845 out of 133,674,966
Mismatches: 9,231,677 out of 133,674,966
Insertions: 991,190 out of 133,674,966

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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 --identity=75..100

Chunking parameters

Hordeum vulgare GoldenPromise Triticum aestivum
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options