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Oryza sativa Japonica Group vs Aegilops tauschii LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 GroupAegilops tauschii
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 325,785 alignment blocks

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

Uncovered: 294,219,203 out of 375,049,285
Covered: 80,830,082 out of 375,049,285

Uncovered: 3,394,683 out of 34,818,902
Matches: 24,406,659 out of 34,818,902
Mismatches: 6,159,986 out of 34,818,902
Insertions: 857,574 out of 34,818,902
Identity over aligned base-pairs: 77.7%

Aegilops tauschii

Uncovered: 4,094,347,807 out of 4,224,915,394
Covered: 130,567,587 out of 4,224,915,394

Uncovered: 8,062,791 out of 53,210,770
Matches: 34,532,047 out of 53,210,770
Mismatches: 9,366,152 out of 53,210,770
Insertions: 1,249,780 out of 53,210,770
Identity over aligned base-pairs: 76.5%

Block size distribution

Size range All 325,785 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,100
11.8 kb
10 bp - 100 bp
54,234
3.6 Mb
30,229
2.1 Mb
100 bp - 1 kb
227,483
83.6 Mb
111,976
38.5 Mb
1 kb - 10 kb
41,912
71.0 Mb
38,395
96.3 Mb
10 kb - 100 kb
54
1.3 Mb
1,357
21.9 Mb
100 kb - 1 Mb
2
250.2 kb
7
942.7 kb