In this section

Triticum aestivum vs Triticum aestivum Renan LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Renan (Triticum aestivum, Triticum_aestivum_Renan_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. Triticum aestivum 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterTriticum aestivumTriticum aestivum Renan
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,468,172 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 2,163,516,282 out of 14,547,261,565
Covered: 12,383,745,283 out of 14,547,261,565

Uncovered: 3,968,018 out of 133,674,966
Matches: 126,680,773 out of 133,674,966
Mismatches: 2,835,940 out of 133,674,966
Insertions: 190,235 out of 133,674,966
Identity over aligned base-pairs: 97.7%

Triticum aestivum Renan

Uncovered: 1,731,115,334 out of 14,195,643,615
Covered: 12,464,528,281 out of 14,195,643,615

Uncovered: 968,521 out of 120,403,789
Matches: 117,825,706 out of 120,403,789
Mismatches: 1,496,345 out of 120,403,789
Insertions: 113,217 out of 120,403,789
Identity over aligned base-pairs: 98.7%

Block size distribution

Size range All 1,468,172 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14,784
88.3 kb
10 bp - 100 bp
243,846
13.1 Mb
104,656
6.1 Mb
100 bp - 1 kb
533,704
201.6 Mb
257,252
93.4 Mb
1 kb - 10 kb
367,897
1.5 Gb
114,239
334.8 Mb
10 kb - 100 kb
294,737
9.5 Gb
8,080
182.4 Mb
100 kb - 1 Mb
13,204
1.7 Gb
577
157.7 Mb
1 Mb - 10 Mb
90
320.7 Mb
10 Mb - 100 Mb
21
474.9 Mb
100 Mb - 1 Gb
21
11.3 Gb