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Oryza longistaminata vs Oryza glumipatula LastZ results

Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Oryza longistaminata 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
HSP threshold (K)3000
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

Chunking parameters

ParameterOryza longistaminataOryza glumipatula
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 298,706 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza longistaminata

Uncovered: 81,425,776 out of 326,442,508
Covered: 245,016,732 out of 326,442,508

Uncovered: 532,955 out of 34,512,301
Matches: 32,665,240 out of 34,512,301
Mismatches: 1,141,760 out of 34,512,301
Insertions: 172,346 out of 34,512,301
Identity over aligned base-pairs: 96.1%

Oryza glumipatula

Uncovered: 164,619,036 out of 372,860,283
Covered: 208,241,247 out of 372,860,283

Uncovered: 6,321,983 out of 41,246,944
Matches: 33,588,726 out of 41,246,944
Mismatches: 1,057,384 out of 41,246,944
Insertions: 278,851 out of 41,246,944
Identity over aligned base-pairs: 96.2%

Block size distribution

Size range All 298,706 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,427
21.2 kb
10 bp - 100 bp
45,588
2.7 Mb
19,616
1.2 Mb
100 bp - 1 kb
185,791
71.1 Mb
84,463
30.7 Mb
1 kb - 10 kb
62,844
162.4 Mb
14,204
34.5 Mb
10 kb - 100 kb
1,056
13.7 Mb
2,964
105.7 Mb
100 kb - 1 Mb
460
77.8 Mb