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Triticum aestivum vs Triticum aestivum Lancer LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Lancer (Triticum aestivum, PGSBv2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. 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 Lancer
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,643,848 alignment blocks

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

Uncovered: 2,500,827,781 out of 14,547,261,565
Covered: 12,046,433,784 out of 14,547,261,565

Uncovered: 2,645,209 out of 133,674,966
Matches: 129,631,964 out of 133,674,966
Mismatches: 1,256,239 out of 133,674,966
Insertions: 141,554 out of 133,674,966
Identity over aligned base-pairs: 98.9%

Triticum aestivum Lancer

Uncovered: 2,262,636,399 out of 14,281,318,419
Covered: 12,018,682,020 out of 14,281,318,419

Uncovered: 9,163,807 out of 175,166,218
Matches: 164,240,714 out of 175,166,218
Mismatches: 1,618,861 out of 175,166,218
Insertions: 142,836 out of 175,166,218
Identity over aligned base-pairs: 98.9%

Block size distribution

Size range All 1,643,848 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16,542
97.9 kb
10 bp - 100 bp
269,037
14.8 Mb
111,947
6.7 Mb
100 bp - 1 kb
621,827
239.3 Mb
290,281
108.3 Mb
1 kb - 10 kb
431,534
1.6 Gb
149,962
418.5 Mb
10 kb - 100 kb
294,324
9.2 Gb
6,945
123.2 Mb
100 kb - 1 Mb
10,584
1.4 Gb
397
155.6 Mb
1 Mb - 10 Mb
205
677.9 Mb
10 Mb - 100 Mb
21
416.7 Mb
100 Mb - 1 Gb
21
10.5 Gb