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 |
|
A15 F8 I1 R1
|
16 |
40.3 |
1420662 |
94.4% |
1341104 |
140.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
2,173,363 |
Δ2 bp |
intergenic (‑1/+1) |
gatC ← / ← gatC |
pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 2,173,361 | 0 | C | . | 95.8%
| 209.9
/ ‑0.2
| 48 | pseudogene (2/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base . (25/21); total (26/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_000913_3_pae_tpiA | 2,173,362 | 0 | C | . | 97.9%
| 209.0
/ ‑2.3
| 48 | pseudogene (1/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (25/21); total (26/22) |
| Fisher's exact test for biased strand distribution p-value = 4.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGG > NC_000913_3_pae_tpiA/2173213‑2173498
||
cGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGCCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACGGCAATTAAAATGGTGCGTGGGATAAAAATCAGGCTTGCCTATacaac > 1:233490/1‑149 (MQ=255)
gAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccg > 1:650661/1‑148 (MQ=255)
aaCAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgc < 2:16094/149‑3 (MQ=255)
cAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccg > 2:612568/1‑145 (MQ=255)
gATTTCCACGAGGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTTGTATAAAAATCAGGCTTGCCGATaccaccgccgta < 2:154877/149‑7 (MQ=255)
tttCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATg > 1:292774/1‑149 (MQ=255)
ccACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTcc > 1:76820/1‑149 (MQ=255)
aCGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCca > 1:22741/1‑149 (MQ=255)
cGATGAACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcag < 1:211749/149‑1 (MQ=255)
aTGCACGGCGACCGTCAGCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca < 1:231690/149‑1 (MQ=255)
tGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagcag < 1:434412/149‑1 (MQ=255)
ccGCCATCGCCACGAAGAAGCAGATGGTGGGAAGATAGCCAAACGGCAGCACCTGATTACCCGGCACAAAAACAGCAATTAAAATGGAGAGTGGGATAAAAATCAGGCTTGCCGATACAA‑‑CCGCCGTATGTCCCAGCGGCAACGCCCGa > 2:121918/1‑149 (MQ=255)
ccATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑Ca > 2:511742/1‑149 (MQ=255)
aTCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACGAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAg > 1:618356/1‑149 (MQ=255)
aTCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAg < 1:503696/149‑1 (MQ=255)
aTCGCCACGAAGAAGCCGATGGGGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACACACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAg < 2:438246/149‑1 (MQ=255)
tCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAgg < 2:650661/149‑1 (MQ=255)
cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCaa > 2:629430/1‑149 (MQ=255)
cACGAAGAAGACGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGTCACACAAACAGCAATTAAAATGGTGAGTGGGATAGAAATCCGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGAAGCAACGCCGGAT‑‑CAAGGCCag > 1:691969/1‑148 (MQ=255)
gCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCACTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCG‑‑ACGCCGCGGCCGTATGTCCCACCAGCAACGCCGGAT‑‑CACGGCCAATCAGGAACt > 1:557684/1‑149 (MQ=255)
gCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACt > 2:703357/1‑149 (MQ=255)
ggCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGAccgc < 2:485162/149‑1 (MQ=255)
aGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGAAA‑‑CCGGATAAGAAGGCCAATCAGGAACTCCTGACCGCCGaa < 1:702631/149‑1 (MQ=255)
aGATCGCCAAACGGCAGCACCGGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCGGGAACTCCTGACCGCCGaa < 2:600152/149‑1 (MQ=255)
ccAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGACGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc > 2:467503/1‑149 (MQ=255)
ccAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCACCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc > 1:282745/1‑149 (MQ=255)
cAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGcc < 2:22741/149‑1 (MQ=255)
aaaCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCt < 1:511742/149‑1 (MQ=255)
aaCGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTg > 1:288557/1‑149 (MQ=255)
agcaCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAGAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCGTGACCGCCGAACTTCGCCTGTAAACg > 2:690492/1‑149 (MQ=255)
aTTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAg > 1:565689/1‑149 (MQ=255)
gCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa < 1:643430/149‑1 (MQ=255)
cacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTCACCGCCGACCTCCGCCTGTAAACGACTACCACCCTGCTTAGCg > 2:573039/1‑149 (MQ=255)
caAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGAt > 2:376572/1‑149 (MQ=255)
aaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATgg < 1:104611/149‑1 (MQ=255)
cAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATc < 1:413576/89‑1 (MQ=255)
cAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATc > 2:413576/1‑89 (MQ=255)
gCAATTAAAATGGTGAGTGGAAAAAAAAGCAGGCTTGCCGATAC‑‑CCCCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGt < 2:661955/149‑1 (MQ=255)
aaTTAAAATGGTGAGTCGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTCCTAGCCTCCTTAGCGATGGGCGttt > 2:235271/1‑148 (MQ=255)
ttAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTaaa > 2:306755/1‑149 (MQ=255)
ttAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTaaa > 2:283221/1‑149 (MQ=255)
aTGGTGAGGGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAccatc < 1:595230/149‑1 (MQ=255)
tGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACCAGCATGATTATCTATGGGCGTTAAACCATCCATGATgg < 1:703357/149‑1 (MQ=255)
gggATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATggg < 2:565689/149‑1 (MQ=255)
aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTaaa > 2:78569/1‑99 (MQ=255)
aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTaaa < 1:78569/99‑1 (MQ=255)
tAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTa > 1:595493/1‑149 (MQ=255)
tAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTa < 1:228227/149‑1 (MQ=255)
aaaaaTCAGGCTTGCCGCTACCA‑‑GCGCCGTATGTCCCAGCAGCAACGCCGAAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGAGCGTTCAACCATCCATGAAGGGTTTaa > 2:129722/1‑149 (MQ=255)
ggCTTGCAGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACGCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGt < 2:233490/149‑1 (MQ=255)
gCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCCCCCGTg > 1:246220/1‑149 (MQ=255)
gCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTg > 1:11168/1‑149 (MQ=255)
cTTGCCGATACCA‑‑ACGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTgg < 2:336257/149‑1 (MQ=255)
||
CGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGAT‑‑CAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGG > NC_000913_3_pae_tpiA/2173213‑2173498
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
