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 |
2,524,241 |
G→T |
39.3% |
V186V (GTC→GTA) ‡ |
yicC ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,524,241 | 0 | G | T | 39.3%
| 49.3
/ 53.8
| 66 | V186V (GTC→GTA) ‡ | yicC | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (25/15); new base T (15/11); total (40/26) |
| Fisher's exact test for biased strand distribution p-value = 7.98e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 |
AGAACCAGTTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACTTCGGCGGT > minE/2524179‑2524309
|
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTTCACCTGATCATCTTCCAGCTTCGCTATCAGa < 1:1702118/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:2468501/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:2048576/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:1727736/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:1652037/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:3312082/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:3296818/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:3226574/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:1308992/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:1278813/69‑1 (MQ=255)
agAACCAACTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCTATCAGa < 1:2922437/69‑1 (MQ=255)
aaCCAGTTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACg < 1:658128/69‑1 (MQ=255)
aCCAGTTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACg > 1:28588/1‑68 (MQ=255)
aCCAGTTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACg > 1:1000886/1‑68 (MQ=255)
tCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGc > 1:2481527/1‑69 (MQ=255)
tCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGc > 1:2305162/1‑69 (MQ=255)
tCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGc > 1:1675186/1‑69 (MQ=255)
tCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGc > 1:2203225/1‑69 (MQ=255)
gCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGc < 1:2600548/68‑1 (MQ=255)
gCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGc < 1:1307316/68‑1 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt > 1:1981414/1‑68 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt > 1:3332848/1‑68 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt < 1:2190083/68‑1 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt < 1:117095/68‑1 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt > 1:831065/1‑68 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt < 1:892304/68‑1 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt > 1:1349681/1‑68 (MQ=255)
ccAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCAt > 1:1597399/1‑68 (MQ=255)
aCGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAg < 1:2790703/69‑1 (MQ=255)
cGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAgg > 1:1177714/1‑69 (MQ=255)
cGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAgg > 1:828634/1‑69 (MQ=255)
cGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAgg > 1:2177041/1‑69 (MQ=255)
cGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAgg > 1:909287/1‑69 (MQ=255)
cGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAgg > 1:2214223/1‑69 (MQ=255)
cGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAgg > 1:1906846/1‑69 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGGGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:1980609/68‑1 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:1582310/68‑1 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:139948/68‑1 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:1498886/68‑1 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:936937/68‑1 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:2229140/68‑1 (MQ=255)
cAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCa < 1:1836165/68‑1 (MQ=255)
cATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACt > 1:2743786/1‑68 (MQ=255)
tCTTACAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTg > 1:2636898/1‑69 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCTGGATTTCCGGCATATGGGAGCGGACTTTGACCACt > 1:1572323/1‑69 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCAc < 1:2075048/68‑1 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACt > 1:947662/1‑69 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACt > 1:3253873/1‑69 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACt > 1:994004/1‑69 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACt > 1:3078824/1‑69 (MQ=255)
aGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACt > 1:2974587/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:1109900/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:1483549/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:1572159/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:1816065/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:1864897/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:2085810/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:798326/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:2116168/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:592282/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:563833/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:2305427/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:2353890/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:2546158/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:2578750/1‑69 (MQ=255)
tCGCTATCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGCGCGGACTTTGGCCACTTcgg > 1:3242057/1‑69 (MQ=255)
gACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACTTCGGCGGt < 1:171369/69‑1 (MQ=255)
gACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACTTCGGCGGt < 1:2783846/69‑1 (MQ=255)
gACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACTTCGGCGGt < 1:3001508/69‑1 (MQ=255)
|
AGAACCAGTTCCTGCTCCAGACGGTTGTTTTCCAGTTGCACCTGAGCATCTTCCAGCTTCGCGACCAGACGCTCACGCTGCCATTGCAGGATTTCCGGCATATGGGAGCGGACTTTGACCACTTCGGCGGT > minE/2524179‑2524309
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
