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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,582,329 |
T→C |
24.6% |
V150V (GTT→GTC) |
gadX → |
DNA‑binding transcriptional dual regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,582,329 | 0 | T | C | 24.6%
| 96.8
/ 27.7
| 81 | V150V (GTT→GTC) | gadX | DNA‑binding transcriptional dual regulator |
| Reads supporting (aligned to +/- strand): ref base T (25/36); new base C (17/3); total (42/39) |
| Fisher's exact test for biased strand distribution p-value = 6.92e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAA > minE/2582263‑2582396
|
tGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGtt > 1:1615107/1‑67 (MQ=255)
tGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGtt > 1:506723/1‑67 (MQ=255)
tGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGtt > 1:797038/1‑67 (MQ=255)
tGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGtt > 1:610360/1‑67 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:339385/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:2014251/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:1587340/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:1574321/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:1535283/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:1617419/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:1657177/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:2789769/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:2946047/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:933632/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:2353162/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:979160/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:2449882/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:3355308/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTACGGTCATCaat > 1:3244140/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTTGCAACCGAATATGCGAACACGAGTTTGTAAGGTCATCaat > 1:2758366/3‑68 (MQ=255)
agtttATACCGTTACTTCTGAACGTGTT‑CAACCGAATATGCGAACACGAGTTTGTACGGTCATCaata > 1:1091671/3‑68 (MQ=255)
cTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataa < 1:668790/69‑1 (MQ=255)
cTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataa < 1:2446172/69‑1 (MQ=255)
tttATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataat < 1:2019718/69‑1 (MQ=255)
tttATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataat < 1:3319692/69‑1 (MQ=255)
tttATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataat < 1:1906454/69‑1 (MQ=255)
tttATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataat < 1:91320/69‑1 (MQ=255)
ttATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataat < 1:2535276/68‑1 (MQ=255)
tataCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataa > 1:1304167/1‑69 (MQ=255)
tataCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataata > 1:756285/1‑68 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:2435347/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:2627952/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:2726521/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:2429221/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:3184684/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:2327746/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:3191550/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:3246171/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:11411/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:563373/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:2194820/68‑1 (MQ=255)
taCCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataat < 1:1629546/68‑1 (MQ=255)
gctgctTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGc < 1:660862/69‑1 (MQ=255)
gAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAg < 1:1588073/67‑1 (MQ=255)
gAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAg < 1:1031805/67‑1 (MQ=255)
gAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAg < 1:480656/67‑1 (MQ=255)
gAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAg < 1:2121405/67‑1 (MQ=255)
aaCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTg > 1:1501409/1‑68 (MQ=255)
aaCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTg > 1:1807584/1‑68 (MQ=255)
aaCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTg > 1:1186314/1‑68 (MQ=255)
aaCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTg > 1:1069895/1‑68 (MQ=255)
aCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataatga < 1:2827977/52‑3 (MQ=255)
aCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataa < 1:3253863/52‑1 (MQ=255)
aCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataa < 1:2537841/52‑1 (MQ=255)
aCGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCaataataa < 1:590771/52‑1 (MQ=255)
ttACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTa < 1:3223901/69‑1 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:659224/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:3429202/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:629165/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:2544909/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:684300/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:2288768/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:218637/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:2070192/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:1923759/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:1662237/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:801980/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:1561937/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:81296/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:829296/1‑35 (MQ=255)
cGAACATGCGAACACGAGTTTGTACGGTTATCaat > 1:896841/1‑35 (MQ=255)
cGAACATGCGAAAACGAGTTTGTACGGTTATCaat > 1:1042622/1‑35 (MQ=255)
cGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCa > 1:1327976/1‑67 (MQ=255)
acGAGTTTGTACGGTCATCAATAATAATATCGCCCATGAGTGGACATTAGCCCGAATTGCTAGCGaatt < 1:99331/69‑4 (MQ=255)
acGAGTTTGTACGGTCATCAATAATAATATCGCCCATGAGTGGACATTAGCCCGAATTGCTAGCGaatt < 1:2229938/69‑4 (MQ=255)
acGAGTTTGTACGGTCATCAATAATAATATCGCCCATGAGTGGACATTAGCCCGAATTGCTAGCGaatt < 1:1601944/69‑4 (MQ=255)
aGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGtt < 1:1105265/69‑1 (MQ=255)
aGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGtt < 1:1154171/69‑1 (MQ=255)
aGTTTGTACGGTTATCAATAATAATATAGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGtt < 1:1244679/69‑1 (MQ=255)
tttGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTtg > 1:2183397/1‑68 (MQ=255)
tttGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTtg > 1:822198/1‑68 (MQ=255)
ttGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTtgat < 1:3375669/69‑1 (MQ=255)
ttGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTtgat < 1:1267447/69‑1 (MQ=255)
ttGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTtgat < 1:673702/69‑1 (MQ=255)
ttGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTtgat < 1:2770534/69‑1 (MQ=255)
ttATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCaa > 1:1389117/1‑69 (MQ=255)
ttATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCaa > 1:676714/1‑69 (MQ=255)
ttATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCaa > 1:381094/1‑69 (MQ=255)
ttATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCa > 1:2317682/1‑68 (MQ=255)
ttATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCa > 1:96884/1‑68 (MQ=255)
|
TGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAA > minE/2582263‑2582396
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
