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Oryza sativa Japonica Group vs Eragrostis tef LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Eragrostis tef (Eragrostis tef, Salk_teff_dabbi_3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 110. 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 GroupEragrostis tef
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 344,307 alignment blocks

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

Uncovered: 290,569,836 out of 375,049,285
Covered: 84,479,449 out of 375,049,285

Uncovered: 3,441,570 out of 34,818,902
Matches: 24,361,241 out of 34,818,902
Mismatches: 6,162,923 out of 34,818,902
Insertions: 853,168 out of 34,818,902
Identity over aligned base-pairs: 77.6%

Eragrostis tef

Uncovered: 431,847,380 out of 575,076,302
Covered: 143,228,922 out of 575,076,302

Uncovered: 16,313,077 out of 79,963,174
Matches: 49,107,416 out of 79,963,174
Mismatches: 13,048,997 out of 79,963,174
Insertions: 1,493,684 out of 79,963,174
Identity over aligned base-pairs: 77.2%

Block size distribution

Size range All 344,307 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,642
28.7 kb
10 bp - 100 bp
70,856
3.8 Mb
13,634
967.0 kb
100 bp - 1 kb
218,944
83.7 Mb
57,162
19.4 Mb
1 kb - 10 kb
48,850
84.0 Mb
19,749
45.1 Mb
10 kb - 100 kb
15
242.1 kb
514
12.6 Mb
100 kb - 1 Mb
51
20.3 Mb
1 Mb - 10 Mb
25
73.4 Mb