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Hordeum vulgare vs Triticum aestivum LastZ Results

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Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Triticum aestivum (Triticum aestivum, IWGSC) 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: 6,002,378

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

Uncovered: 3,691,532,476 out of 4,833,907,081
Covered: 1,142,374,605 out of 4,833,907,081

Uncovered: 1,616,305 out of 44,392,268
Matches: 38,178,870 out of 44,392,268
Mismatches: 4,004,501 out of 44,392,268
Insertions: 592,592 out of 44,392,268

Triticum aestivum

Uncovered: 11,452,554,775 out of 14,547,261,565
Covered: 3,094,706,790 out of 14,547,261,565

Uncovered: 5,314,235 out of 136,655,258
Matches: 112,863,839 out of 136,655,258
Mismatches: 17,064,308 out of 136,655,258
Insertions: 1,412,876 out of 136,655,258

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=3000 --inner=2200 --ambiguous=iupac

Chunking parameters

Hordeum vulgare Triticum aestivum
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}