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 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,948,123 |
T→C |
21.4% |
T40A (ACC→GCC) |
yjjB ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,948,123 | 0 | T | C | 21.4%
| 114.5
/ 28.3
| 56 | T40A (ACC→GCC) | yjjB | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (20/24); new base C (4/8); total (24/32) |
| Fisher's exact test for biased strand distribution p-value = 5.25e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTTTACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAG > minE/2948054‑2948188
|
tttttACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTa < 1:518001/71‑1 (MQ=255)
tttttACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTa < 1:496285/71‑1 (MQ=255)
tttttACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTa < 1:411873/71‑1 (MQ=255)
ttttACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTa < 1:2938057/70‑1 (MQ=255)
ccgccgAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAaca > 1:2661766/1‑69 (MQ=255)
ccgccgAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACt > 1:642868/1‑71 (MQ=255)
aaaTCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGa < 1:3538970/71‑1 (MQ=255)
ttGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGcc < 1:3212597/71‑1 (MQ=255)
gCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCa < 1:1166526/70‑1 (MQ=255)
gCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGCCCGCCACGGTAAACACTTTCGGATGCGCCa < 1:1372336/70‑1 (MQ=255)
cGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGa < 1:3742606/71‑1 (MQ=255)
gTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTa < 1:3684302/48‑1 (MQ=255)
gTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTa < 1:2957219/48‑1 (MQ=255)
tataAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCg < 1:4012228/57‑1 (MQ=255)
tataAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCg < 1:1818886/57‑1 (MQ=255)
tataAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATAc < 1:1711145/71‑1 (MQ=255)
aaGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCa < 1:2952528/63‑1 (MQ=255)
gCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAgcg > 1:3875810/1‑71 (MQ=255)
tatGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGAcc < 1:2816640/71‑1 (MQ=255)
tatGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGAc > 1:3657785/1‑70 (MQ=255)
tatGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGAc > 1:678507/1‑70 (MQ=255)
tatGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATg > 1:3880376/1‑51 (MQ=255)
tatGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGAcg < 1:1255878/71‑2 (MQ=255)
tatGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGAcc < 1:3180287/71‑1 (MQ=255)
cccGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTg < 1:882575/71‑1 (MQ=255)
aaCATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATAc > 1:2833473/1‑70 (MQ=255)
aTAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAAt < 1:2227611/71‑1 (MQ=255)
aGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCaa > 1:3007944/1‑68 (MQ=255)
gggATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCaa > 1:378934/1‑67 (MQ=255)
gggATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATgg > 1:3961345/1‑70 (MQ=255)
gggATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATgg > 1:1439498/1‑70 (MQ=255)
gATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTAc > 1:2155132/1‑71 (MQ=255)
tAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGaa < 1:1078935/57‑1 (MQ=255)
tAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTAcc > 1:2578332/1‑70 (MQ=255)
tAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATAc < 1:779895/41‑1 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATa > 1:3480681/1‑57 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGAc < 1:2528021/71‑1 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGAc > 1:781231/1‑71 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGAc > 1:2266861/1‑71 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGAc < 1:557589/71‑1 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGAc < 1:74928/71‑1 (MQ=255)
gccgccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAg > 1:57997/1‑71 (MQ=255)
gccgccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAg < 1:3485719/71‑1 (MQ=255)
gccgccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAg > 1:3307186/1‑71 (MQ=255)
cgccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa > 1:3155519/1‑71 (MQ=255)
cgccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa > 1:831791/1‑71 (MQ=255)
gccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa > 1:1964098/1‑70 (MQ=255)
gccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa > 1:3232811/1‑70 (MQ=255)
gccACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa > 1:658575/1‑70 (MQ=255)
cACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAg < 1:1386669/71‑1 (MQ=255)
cACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAg < 1:3992100/71‑1 (MQ=255)
cACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAg < 1:2918722/71‑1 (MQ=255)
cACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAg < 1:2768833/71‑1 (MQ=255)
cACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAg < 1:2407658/71‑1 (MQ=255)
aCGGTAAACACTTTCGGATGCGCCAGATACCATCGCGACCATTGAATACCAATGGTACCGACCAGCATAg > 1:1881178/1‑70 (MQ=255)
cGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATAcc < 1:2078192/49‑1 (MQ=255)
|
TTTTTACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAG > minE/2948054‑2948188
|
| 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
