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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-1B1 var. IR64) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-1B1 var. IR64) (Oryza sativa Indica Group, OsIR64RS1) 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-1B1 var. IR64)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 119,566 alignment blocks

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

Uncovered: 69,147,321 out of 375,049,285
Covered: 305,901,964 out of 375,049,285

Uncovered: 386,847 out of 34,818,902
Matches: 34,008,735 out of 34,818,902
Mismatches: 353,661 out of 34,818,902
Insertions: 69,659 out of 34,818,902
Identity over aligned base-pairs: 98.8%

Oryza sativa (Xian/Indica-1B1 var. IR64)

Uncovered: 80,569,918 out of 387,434,309
Covered: 306,864,391 out of 387,434,309

Uncovered: 287,275 out of 42,081,291
Matches: 41,163,819 out of 42,081,291
Mismatches: 532,326 out of 42,081,291
Insertions: 97,871 out of 42,081,291
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 119,566 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,360
8.0 kb
10 bp - 100 bp
25,071
1.4 Mb
11,843
723.1 kb
100 bp - 1 kb
57,072
20.5 Mb
26,862
9.6 Mb
1 kb - 10 kb
26,970
96.7 Mb
7,814
18.0 Mb
10 kb - 100 kb
8,951
192.0 Mb
310
6.0 Mb
100 kb - 1 Mb
142
22.2 Mb
19
3.8 Mb
1 Mb - 10 Mb
1
3.1 Mb
10 Mb - 100 Mb
12
291.5 Mb