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 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,948,123 |
T→C |
27.5% |
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 | 27.5%
| 60.1
/ 26.9
| 40 | T40A (ACC→GCC) | yjjB | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (16/13); new base C (5/6); total (21/19) |
| Fisher's exact test for biased strand distribution p-value = 7.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
TTTACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAGAAGC > minE/2948056‑2948192
|
tttACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTaaa > 1:1065692/1‑71 (MQ=255)
tACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAac < 1:1808196/70‑1 (MQ=255)
aaaTCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCgg < 1:329183/70‑1 (MQ=255)
aTCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATg > 1:529287/1‑71 (MQ=255)
cATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATgcg > 1:636044/1‑71 (MQ=255)
gCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCa < 1:357530/70‑1 (MQ=255)
cGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAg < 1:34288/70‑1 (MQ=255)
cGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAg < 1:1587784/70‑1 (MQ=255)
gTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATa > 1:979247/1‑71 (MQ=255)
ataAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACt < 1:708836/52‑1 (MQ=255)
taAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATAc > 1:996003/1‑69 (MQ=255)
taAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTc > 1:1585786/1‑54 (MQ=255)
aaGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAg > 1:1238229/1‑71 (MQ=255)
aGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTaaa > 1:147950/1‑45 (MQ=255)
ccGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAgcgc < 1:2068456/71‑1 (MQ=255)
cGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAGcgcg < 1:1144218/71‑1 (MQ=255)
tGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCa < 1:155193/70‑1 (MQ=255)
cccGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCAtt > 1:306801/1‑70 (MQ=255)
cccGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTg < 1:103756/71‑1 (MQ=255)
ccGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGa < 1:1749100/71‑1 (MQ=255)
ggggAACATAGGGATAACGGCCGCCACTGTAAACACTTTCGGATGGGCCAGATACCAGCGCGACCa < 1:1732895/65‑1 (MQ=255)
cGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTg < 1:1325620/69‑1 (MQ=255)
gggAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGaa > 1:1445574/1‑70 (MQ=255)
ggAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGaa > 1:137336/1‑69 (MQ=255)
gAACATAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCAt > 1:1806752/1‑64 (MQ=255)
aaCATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATAcc < 1:785787/71‑1 (MQ=255)
aaCATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATAc > 1:835323/1‑70 (MQ=255)
tAGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATg > 1:1987104/1‑71 (MQ=255)
aGGGATAACGGCCGCCACGGTAAACACTTTCGGATg > 1:1666729/1‑36 (MQ=255)
aGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTg > 1:1659293/1‑60 (MQ=255)
aGGGATAACGGCCGCCACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGAcc > 1:2034600/1‑56 (MQ=255)
gggATAACGGCCGCCACGGTAAACACTTTCTGATGCGCCAGATACCAGCGCGa > 1:2107659/1‑53 (MQ=255)
gggATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGt < 1:681649/71‑1 (MQ=255)
aCGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGaaaa > 1:1263009/1‑55 (MQ=255)
cgccACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa < 1:1960771/71‑1 (MQ=255)
cgccACGGCAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCa < 1:2074355/71‑1 (MQ=255)
aCGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGaa > 1:1147334/1‑46 (MQ=255)
aCGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAGa < 1:1320729/71‑1 (MQ=255)
gTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTg < 1:57756/41‑1 (MQ=255)
gTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAGAAGc > 1:498561/1‑71 (MQ=255)
|
TTTACCGCCGAAATCATTGCGGTATAAGCCGATATGCCCGGGAACATAGGGATAACGGCCGCCACGGTAAACACTTTCGGATGCGCCAGATACCAGCGCGACCATTGAATACCAATGGTACCGACCAGCATAGAAGC > minE/2948056‑2948192
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
