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Triticum aestivum vs Triticum aestivum Julius LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Julius (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 Julius
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,559,388 alignment blocks

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

Uncovered: 2,218,435,348 out of 14,547,261,565
Covered: 12,328,826,217 out of 14,547,261,565

Uncovered: 2,776,274 out of 133,674,966
Matches: 129,606,701 out of 133,674,966
Mismatches: 1,166,053 out of 133,674,966
Insertions: 125,938 out of 133,674,966
Identity over aligned base-pairs: 99.0%

Triticum aestivum Julius

Uncovered: 2,050,818,000 out of 14,385,030,226
Covered: 12,334,212,226 out of 14,385,030,226

Uncovered: 8,101,553 out of 176,371,410
Matches: 166,603,629 out of 176,371,410
Mismatches: 1,522,351 out of 176,371,410
Insertions: 143,877 out of 176,371,410
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,559,388 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15,881
95.3 kb
10 bp - 100 bp
256,781
14.0 Mb
106,386
6.4 Mb
100 bp - 1 kb
551,386
209.1 Mb
263,035
96.4 Mb
1 kb - 10 kb
409,023
1.6 Gb
119,197
335.1 Mb
10 kb - 100 kb
317,022
9.7 Gb
5,640
105.1 Mb
100 kb - 1 Mb
9,295
1.2 Gb
368
138.0 Mb
1 Mb - 10 Mb
107
379.8 Mb
10 Mb - 100 Mb
21
428.5 Mb
100 Mb - 1 Gb
21
11.2 Gb