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Arabidopsis thaliana vs Camelina sativa LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Camelina sativa (Camelina sativa, Cs) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. Arabidopsis thaliana 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

ParameterArabidopsis thalianaCamelina sativa
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 586,919 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 25,428,715 out of 119,667,750
Covered: 94,239,035 out of 119,667,750

Uncovered: 677,188 out of 33,775,569
Matches: 27,221,534 out of 33,775,569
Mismatches: 5,522,491 out of 33,775,569
Insertions: 354,356 out of 33,775,569
Identity over aligned base-pairs: 82.2%

Camelina sativa

Uncovered: 307,128,401 out of 641,356,059
Covered: 334,227,658 out of 641,356,059

Uncovered: 9,788,254 out of 107,028,261
Matches: 85,431,311 out of 107,028,261
Mismatches: 10,482,856 out of 107,028,261
Insertions: 1,325,840 out of 107,028,261
Identity over aligned base-pairs: 87.9%

Block size distribution

Size range All 586,919 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8,868
51.4 kb
10 bp - 100 bp
128,285
6.9 Mb
38,186
2.6 Mb
100 bp - 1 kb
348,362
128.1 Mb
168,545
59.6 Mb
1 kb - 10 kb
101,212
229.4 Mb
35,038
80.8 Mb
10 kb - 100 kb
192
2.3 Mb
402
9.9 Mb
100 kb - 1 Mb
72
24.1 Mb
1 Mb - 10 Mb
38
155.0 Mb
10 Mb - 100 Mb
3
34.8 Mb