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 |
|
A25 F36 I0 R2
|
1302 |
104.9 |
4551290 |
96.3% |
4382892 |
111.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,463,480 |
Δ1 bp |
13.4% |
intergenic (+42/‑59) |
paaK → / → paaX |
phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,463,480 | 0 | A | . | 13.4%
| 227.2
/ 30.0
| 67 | intergenic (+42/‑59) | paaK/paaX | phenylacetyl‑CoA ligase/transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| Reads supporting (aligned to +/- strand): ref base A (28/30); new base . (4/5); total (32/35) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
TCTCTACCGATGTGATGATCGTTAACTGTGGCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAGTGGCACATCTTTGATCTC > NC_000913/1463341‑1463609
|
tctcTACCGATGTGATGATCGTTAACTGTGGCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTcgatac < 2:973960‑M2/148‑7 (MQ=255)
tctACCGATGTGATGATCGTTAACTGTGGCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGa < 1:1008694/148‑1 (MQ=255)
atCGTTAACTGTGGCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTc < 1:973960/148‑1 (MQ=255)
ggCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATg < 4:496530/132‑1 (MQ=255)
ggCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATg > 3:496530/1‑132 (MQ=255)
cAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCAcaacaa > 1:409625/1‑148 (MQ=255)
aGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAAt > 1:1043294/1‑148 (MQ=255)
aaggcGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATg < 2:1043294/148‑1 (MQ=255)
tgtCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTaaa < 2:409625/148‑1 (MQ=255)
cGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAg < 1:171501/79‑1 (MQ=255)
cGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAg > 2:171501/1‑79 (MQ=255)
gcAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAg > 2:447631/1‑110 (MQ=255)
gcAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAg < 1:447631/110‑1 (MQ=255)
tGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTcgatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcacatcggta < 2:396354‑M2/148‑102 (MQ=255)
gACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTcgatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggata > 3:343372‑M2/1‑46 (MQ=255)
gACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTcgatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggata < 4:343372‑M2/117‑72 (MQ=255)
aCGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGa > 2:1061698/1‑101 (MQ=255)
aCGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGa < 1:1061698/101‑1 (MQ=255)
tCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATaa > 4:1056002/1‑77 (MQ=255)
tCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATaa > 4:1130786/1‑77 (MQ=255)
tCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATaa < 3:1130786/77‑1 (MQ=255)
tCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATaa < 3:1056002/77‑1 (MQ=255)
cTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt > 2:159422/1‑110 (MQ=255)
cTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt < 1:159422/110‑1 (MQ=255)
tGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcgcatcggtagagatccccaccatc < 2:1002090‑M2/148‑116 (MQ=255)
ggCCCTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaa < 3:532854‑M2/115‑84 (MQ=255)
ggCCCTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaa > 4:532854‑M2/1‑32 (MQ=255)
gCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATAc < 4:523393/106‑1 (MQ=255)
gCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATAc > 3:523393/1‑106 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGAAGTcgatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcacatcggtagagatccccaccatcga > 1:396354‑M2/1‑30 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt < 1:974691/104‑1 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt > 2:974691/1‑104 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAGTGGCACATc > 1:657789/1‑148 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcacatcggtagagatcc > 1:962068‑M2/1‑28 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcacatcggtagagatcc < 2:962068‑M2/135‑108 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaa < 2:468484‑M2/63‑36 (MQ=255)
cTGGTGGGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaa > 1:468484‑M2/1‑28 (MQ=255)
tggtggGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTaaa < 2:690522/123‑1 (MQ=255)
tggtggGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTaaa > 1:690522/1‑123 (MQ=255)
ggtggGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCa > 3:702487/1‑110 (MQ=255)
ggtggGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCa < 4:702487/110‑1 (MQ=255)
ggtggGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcacatcggtagagatccccaccatcgacttaa < 4:187228‑M2/148‑123 (MQ=255)
gtggGGTAAAGCGCCAGGGCCAGA‑‑gatacgtcaggcaccaacaatattgcgcagatcaaacacccgacacgccttgccttctgaacgcgggatactgccacagttaacgatcatcacatcggtagagatccccaccatcgacttaat > 3:187228‑M2/1‑25 (MQ=255)
ggggTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAGTGGCACATCTTTGa < 2:657789/148‑1 (MQ=255)
gTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTcc > 2:949017/1‑125 (MQ=255)
gTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTcc < 1:949017/125‑1 (MQ=255)
tAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACt < 2:474432/88‑1 (MQ=255)
tAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACt > 1:474432/1‑88 (MQ=255)
tAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAg < 4:961670/130‑1 (MQ=255)
tAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAg > 3:961670/1‑130 (MQ=255)
tAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAGTGGCACATCTTTGAtctc > 1:291769/1‑148 (MQ=255)
aaaGCGCCAGGGCTAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTaaa > 3:77455/1‑114 (MQ=255)
aaaGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTaaa < 4:77455/114‑1 (MQ=255)
aGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGa < 4:112128/69‑1 (MQ=255)
aGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGa > 3:112128/1‑69 (MQ=255)
gcgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACCGACTGAAGCGAATGAGTAAACTTg < 2:417160/86‑1 (MQ=255)
gcgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTg > 1:417160/1‑86 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt < 2:302089/90‑1 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt < 4:355096/90‑1 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt > 1:302089/1‑90 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt > 3:355096/1‑90 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTa < 3:788131/94‑1 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTa > 4:788131/1‑94 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTaa > 2:108851/1‑109 (MQ=255)
cgcCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTaa < 1:108851/109‑1 (MQ=255)
gAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt > 4:1118803/1‑79 (MQ=255)
gAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACt < 3:1118803/79‑1 (MQ=255)
|
TCTCTACCGATGTGATGATCGTTAACTGTGGCAGTATCCCGCGTTCAGAAGGCAAGGCGTGTCGGGTGTTTGATCTGCGCAATATTGTTGGTGCCTGACGTATCGTCTGGCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGATACGACCTGTGCTATGATTCATAAATCACAACAATAACAACAGACTGAAGCGAATGAGTAAACTTGATACTTTTATCCAACATGCTGTAAACGCTGTTCCGGTCAGTGGCACATCTTTGATCTC > NC_000913/1463341‑1463609
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
