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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-2B var. Larha Mugad) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-2B var. Larha Mugad) (Oryza sativa Indica Group, Os125619RS1) 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 (Xian/Indica-2B var. Larha Mugad)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 120,570 alignment blocks

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

Uncovered: 66,372,084 out of 375,049,285
Covered: 308,677,201 out of 375,049,285

Uncovered: 338,625 out of 34,818,902
Matches: 34,078,339 out of 34,818,902
Mismatches: 332,672 out of 34,818,902
Insertions: 69,266 out of 34,818,902
Identity over aligned base-pairs: 98.8%

Oryza sativa (Xian/Indica-2B var. Larha Mugad)

Uncovered: 81,954,579 out of 391,869,645
Covered: 309,915,066 out of 391,869,645

Uncovered: 324,906 out of 41,893,402
Matches: 40,949,811 out of 41,893,402
Mismatches: 520,436 out of 41,893,402
Insertions: 98,249 out of 41,893,402
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 120,570 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,385
8.1 kb
10 bp - 100 bp
24,866
1.4 Mb
11,728
713.1 kb
100 bp - 1 kb
56,111
20.1 Mb
26,234
9.3 Mb
1 kb - 10 kb
28,843
104.3 Mb
7,484
17.2 Mb
10 kb - 100 kb
9,277
194.7 Mb
338
6.5 Mb
100 kb - 1 Mb
88
14.1 Mb
13
2.8 Mb
1 Mb - 10 Mb
1
3.0 Mb
10 Mb - 100 Mb
12
295.2 Mb