Medicago truncatula vs Glycine max LastZ results
Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Medicago truncatula 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
Parameter | Value |
---|---|
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
Parameter | Medicago truncatula | Glycine max |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 586,842 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Medicago truncatula |
Uncovered: 297,140,757 out of 412,800,391 |
Uncovered: 9,348,669 out of 50,132,764 |
Glycine max |
Uncovered: 780,193,479 out of 978,491,270 |
Uncovered: 5,195,015 out of 65,618,132 |
Block size distribution
Size range | All 586,842 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 7,670 |
45.7 kb |
|||
10 bp - 100 bp | 107,077 |
6.3 Mb |
34,362 |
2.4 Mb |
|
100 bp - 1 kb | 416,802 |
152.4 Mb |
154,216 |
50.1 Mb |
|
1 kb - 10 kb | 55,100 |
89.9 Mb |
29,232 |
70.6 Mb |
|
10 kb - 100 kb | 191 |
4.1 Mb |
1,108 |
26.0 Mb |
|
100 kb - 1 Mb | 2 |
201.0 kb |
122 |
38.3 Mb |
|
1 Mb - 10 Mb | 36 |
65.5 Mb |