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Oryza sativa Japonica Group vs Echinochloa crus-galli LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Echinochloa crus-galli (Echinochloa crus-galli, ec_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 107. 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 GroupEchinochloa crus-galli
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 511,390 alignment blocks

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

Uncovered: 287,037,293 out of 375,049,285
Covered: 88,011,992 out of 375,049,285

Uncovered: 3,185,242 out of 34,424,450
Matches: 24,415,013 out of 34,424,450
Mismatches: 6,015,344 out of 34,424,450
Insertions: 808,851 out of 34,424,450
Identity over aligned base-pairs: 78.2%

Echinochloa crus-galli

Uncovered: 1,115,418,498 out of 1,340,710,827
Covered: 225,292,329 out of 1,340,710,827

Uncovered: 45,941,740 out of 131,940,077
Matches: 67,356,237 out of 131,940,077
Mismatches: 16,446,535 out of 131,940,077
Insertions: 2,195,565 out of 131,940,077
Identity over aligned base-pairs: 78.3%

Block size distribution

Size range All 511,390 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,747
39.6 kb
10 bp - 100 bp
99,677
5.4 Mb
21,462
1.5 Mb
100 bp - 1 kb
329,450
125.7 Mb
100,455
34.0 Mb
1 kb - 10 kb
74,507
129.2 Mb
30,426
71.1 Mb
10 kb - 100 kb
9
126.8 kb
873
21.4 Mb
100 kb - 1 Mb
83
32.6 Mb
1 Mb - 10 Mb
33
99.9 Mb