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Oryza sativa Japonica Group vs Trifolium pratense LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Trifolium pratense (Trifolium pratense, Trpr) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 GroupTrifolium pratense
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 140,564 alignment blocks

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

Uncovered: 343,357,036 out of 375,049,285
Covered: 31,692,249 out of 375,049,285

Uncovered: 16,336,840 out of 34,818,902
Matches: 11,594,252 out of 34,818,902
Mismatches: 6,503,478 out of 34,818,902
Insertions: 384,332 out of 34,818,902
Identity over aligned base-pairs: 62.7%

Trifolium pratense

Uncovered: 272,193,050 out of 304,842,038
Covered: 32,648,988 out of 304,842,038

Uncovered: 20,205,561 out of 41,242,947
Matches: 13,496,534 out of 41,242,947
Mismatches: 7,121,210 out of 41,242,947
Insertions: 419,642 out of 41,242,947
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 140,564 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,029
5.1 kb
1
5.0 bp
10 bp - 100 bp
22,295
1.6 Mb
5,119
369.8 kb
100 bp - 1 kb
109,930
34.9 Mb
32,527
12.8 Mb
1 kb - 10 kb
7,277
11.3 Mb
16,195
34.1 Mb
10 kb - 100 kb
33
356.0 kb
70
892.9 kb