Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A16 F3 I1 R1
|
16 |
53.0 |
1853282 |
94.4% |
1749498 |
141.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
3,560,455 |
+G |
intergenic (‑2/+1) |
glpR ← / ← glpR |
pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 3,560,455 | 1 | . | G | 94.4%
| 107.5
/ ‑0.0
| 37 | intergenic (‑2/+1) | glpR/glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (14/20); total (14/23) |
| Fisher's exact test for biased strand distribution p-value = 5.11e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTG > NC_000913_3_pae_tpiA/3560316‑3560593
|
gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGCATGGCGTTGCGTTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGGTCa > 2:797736/1‑149 (MQ=255)
aGCGTCGCGCCATTGGGGATTTGCTCCGCCCCTGTGCGGGCCATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCTACTGCGTGTTAACCGATCTGGAAGGAAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTg < 1:387528/149‑1 (MQ=255)
gCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGc < 1:538932/149‑1 (MQ=255)
aTTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg < 1:463977/149‑1 (MQ=255)
aTTTGCTCCGCCACTTGGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAg < 1:925959/149‑1 (MQ=255)
tttGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAgg > 1:678684/1‑149 (MQ=255)
cACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGaa < 1:699082/149‑1 (MQ=255)
ttttGCTGGTGATGCGCTGTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCTGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa < 2:19444/148‑1 (MQ=255)
gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt > 2:914332/1‑123 (MQ=255)
gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt < 1:914332/123‑1 (MQ=255)
ttttCTTCCGTCTGGGTGGCCTTCGGATCGTGCCACGGCGGGTTAACCGAACTGGAAGGCAGCGCCCCCCCGCCCTGCCA‑ACC‑CCGGCTCAGGTTGTGCGCCTCCAGCTCATTGAGGTCGCGCCGAATAGCCTGCGGGCTGACGGAGaa < 2:433240/149‑1 (MQ=255)
tttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa > 1:770027/1‑149 (MQ=255)
gcttcGGTCTGGGTGGCCGTGCGATCGTGCCACGGCGTGGTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATg < 2:858477/148‑1 (MQ=255)
ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct > 1:88936/1‑149 (MQ=255)
ggTCCGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTa < 1:205185/149‑1 (MQ=255)
gggTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGc < 1:772245/149‑1 (MQ=255)
atGGCCTTGCGATCGTGCCACGGCGTGTCAACCGAACTGGAAAGCAGCGCCGCACCGCCCTG‑AT‑AGCGCACGATCAAGTCTTGCTCCGCCACCAGATTAGGGTCGCGGCGAATAGTCTGCGCGCCGACGGAGACATGCCCTACCAGccc > 2:703034/2‑147 (MQ=255)
ggCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt < 1:189668/149‑1 (MQ=255)
tcTTGCGGTCGTGCGGCGGGGTGTTAATCGAACTGGAAGGCAGCGCCGCACCGCTATG‑GT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg < 2:804719/148‑1 (MQ=255)
ccTTGGGATCGTGCCACGGCGTGTTAACCGACCTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg < 2:132895/149‑1 (MQ=255)
cTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCCCTACCAGCTCTTCgg > 1:923656/1‑149 (MQ=255)
ttGGGATCGTGCCCCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCAGG‑AT‑GCCGCAGGAGCAGGGTTTGCGCCGCCAGCTCATTGAGGGCGCCGCGAATTGTCTGCGGCGCGACGGAGATATGATCTACCAGCTCTTCgtt > 2:442404/1‑147 (MQ=255)
tCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc < 2:770027/149‑1 (MQ=255)
tCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc > 2:883730/1‑149 (MQ=255)
ccACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAACTCTTCGGTACTGACATAAc > 2:669071/1‑149 (MQ=255)
cccGGCGTTTTAACCGAACTGGAAGGCAGCGCCGCTCCGTCATG‑AC‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc < 1:797736/147‑1 (MQ=255)
cGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg < 1:846379/102‑1 (MQ=255)
cGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg > 2:846379/1‑102 (MQ=255)
cGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg > 2:846398/1‑102 (MQ=255)
cGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg < 1:846398/102‑1 (MQ=255)
tcgttctAACCAAAGTGGAAGTCTGCGGCGGACAGCCATG‑ATGGGG‑GAGGTTCAGTTTTTTGTCCGTAAGGTCTTAGAGGTCGAGGCAAATAGTCTTCGCTTTGCCTTAGTAATGCTCTACCAGCACTTCGGTACTGACATAACCctgc < 2:767481/143‑1 (MQ=255)
gtAACCGGACGGGAAGGCAGGGGCGAACCGCCATG‑AG‑GGCGCGGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt < 2:143366/148‑1 (MQ=255)
aCCGAGCGGGAAGGCAGCGCCGTGCCGTCATG‑GT‑GGCTGAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGGCGCTAATAGTCTGCGGGCTGACGGAGATATGCTCTACCAGCTCTTCGGTACTGCCATAAGCCTGCTGTTTGAc < 2:623108/149‑1 (MQ=255)
cccgaACCGCCATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGtt < 1:44783/148‑1 (MQ=255)
ccATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAGTCTCTACCAGCTCTTCGGTACTGACATAACCCTGCGGTTTAACAAGTTCGCTAATACCGTTGTGACGTtg > 2:151019/1‑149 (MQ=255)
cATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa < 2:584107/107‑1 (MQ=255)
cATG‑AT‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATaa > 1:584107/1‑107 (MQ=255)
|
GATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATG‑AT‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTG > NC_000913_3_pae_tpiA/3560316‑3560593
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
