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Oryza sativa Japonica Group vs Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka) (Oryza sativa tropical japonica subgroup, Os128077RS1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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
HSP threshold (K)
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 sativa Japonica GroupOryza sativa (Geng/Japonica-trop2 var. Ketan Nangka)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 68,313 alignment blocks

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

Uncovered: 38,860,694 out of 375,049,285
Covered: 336,188,591 out of 375,049,285

Uncovered: 213,450 out of 34,818,902
Matches: 34,388,799 out of 34,818,902
Mismatches: 182,216 out of 34,818,902
Insertions: 34,437 out of 34,818,902
Identity over aligned base-pairs: 99.4%

Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka)

Uncovered: 44,905,209 out of 382,007,384
Covered: 337,102,175 out of 382,007,384

Uncovered: 158,262 out of 42,310,722
Matches: 41,785,635 out of 42,310,722
Mismatches: 312,569 out of 42,310,722
Insertions: 54,256 out of 42,310,722
Identity over aligned base-pairs: 99.1%

Block size distribution

Size range All 68,313 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
819
4.7 kb
10 bp - 100 bp
14,255
820.4 kb
7,029
432.0 kb
100 bp - 1 kb
32,881
11.7 Mb
15,979
5.6 Mb
1 kb - 10 kb
14,121
48.8 Mb
4,811
11.1 Mb
10 kb - 100 kb
5,470
157.7 Mb
227
4.7 Mb
100 kb - 1 Mb
767
138.8 Mb
10
2.1 Mb
1 Mb - 10 Mb
1
2.9 Mb
10 Mb - 100 Mb
12
330.9 Mb