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Oryza sativa Japonica Group vs Hordeum vulgare LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, MorexV3_pseudomolecules_assembly) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 105. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

Chunking parameters

ParameterOryza sativa Japonica GroupHordeum vulgare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 259,714 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 298,751,736 out of 375,049,285
Covered: 76,297,549 out of 375,049,285

Uncovered: 3,895,366 out of 34,818,902
Matches: 23,999,767 out of 34,818,902
Mismatches: 6,086,776 out of 34,818,902
Insertions: 836,993 out of 34,818,902
Identity over aligned base-pairs: 77.6%

Hordeum vulgare

Uncovered: 4,116,123,552 out of 4,225,577,519
Covered: 109,453,967 out of 4,225,577,519

Uncovered: 7,967,353 out of 42,301,356
Matches: 26,719,516 out of 42,301,356
Mismatches: 6,856,473 out of 42,301,356
Insertions: 758,014 out of 42,301,356
Identity over aligned base-pairs: 77.8%

Block size distribution

Size range All 259,714 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,882
10.6 kb
10 bp - 100 bp
36,048
2.3 Mb
16,068
1.1 Mb
100 bp - 1 kb
184,167
70.1 Mb
83,758
30.5 Mb
1 kb - 10 kb
37,615
63.5 Mb
34,964
86.8 Mb
10 kb - 100 kb
1
31.2 kb
991
16.6 Mb
100 kb - 1 Mb
1
139.5 kb
8
1.1 Mb