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 |
1,556,777 |
T→C |
29.3% |
intergenic (+627/+636) |
dsdA → / ← emrY |
D‑serine ammonia‑lyase/predicted multidrug efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,556,777 | 0 | T | C | 29.3%
| 79.4
/ 38.6
| 85 | intergenic (+627/+636) | dsdA/emrY | D‑serine ammonia‑lyase/predicted multidrug efflux system |
| Reads supporting (aligned to +/- strand): ref base T (22/38); new base C (9/16); total (31/54) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.36e-01 |
ACGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTGG > minE/1556732‑1556836
|
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:126947/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:1377597/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:2970348/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:433479/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:3214120/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:2211043/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:2274814/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:589445/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:233705/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:626874/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:658558/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:2497434/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:2942168/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:1503860/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACCaac < 1:3378364/49‑1 (MQ=255)
aCGCCAGTAATAGCAAACCGCATACAT‑AAAAAACTAAATGTCACCaac < 1:252539/48‑1 (MQ=255)
aGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCAt < 1:2650427/69‑1 (MQ=255)
aGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCAt < 1:143014/69‑1 (MQ=255)
aGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCAt < 1:245852/69‑1 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTAt < 1:155313/55‑1 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCAt > 1:461924/1‑66 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAAc > 1:1972268/1‑69 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAAc > 1:2833064/1‑69 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAAc > 1:1008904/1‑69 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAAc > 1:92107/1‑69 (MQ=255)
aaTAGCAAACCGCATACATCAAAAAACT‑AATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:2669803/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:2236128/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:938050/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:2529811/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:222590/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:2948439/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:310295/1‑69 (MQ=255)
aTAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACg > 1:1901647/1‑69 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:3058930/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:2707986/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:526364/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:1912966/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:1312802/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:386884/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:706072/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATa < 1:1231971/64‑1 (MQ=255)
aGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTc < 1:34126/69‑1 (MQ=255)
gCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTGTATTTTGTTGCCATAACGTcc > 1:1540336/1‑69 (MQ=255)
gCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTcc > 1:1305997/1‑69 (MQ=255)
gCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTcc > 1:1407026/1‑69 (MQ=255)
gCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTcc > 1:3049348/1‑69 (MQ=255)
gCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATATCTATTTTGTTGCCATAACGTcc > 1:2337349/1‑69 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:765848/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:2872814/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:417/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:986761/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:1368144/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:1986195/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:1178061/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:1999087/1‑56 (MQ=255)
aaaCCGCATACATCAAAAAACTAAATGTCACCAACAACCGCATATCAATTttgttg > 1:1099364/1‑56 (MQ=255)
cATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGa > 1:2526061/1‑69 (MQ=255)
cAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGaaa > 1:2632521/1‑68 (MQ=255)
cAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGaa > 1:2020312/1‑67 (MQ=255)
cAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGaa > 1:2557765/1‑67 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:1312115/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:3189496/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:2628363/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:3228240/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:2219990/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:1506203/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:368698/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTaa < 1:149749/69‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTa < 1:1356420/68‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTa < 1:433550/68‑1 (MQ=255)
aaaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTa < 1:13680/68‑1 (MQ=255)
aaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAAt < 1:1208373/69‑1 (MQ=255)
aaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAAt < 1:1091941/69‑1 (MQ=255)
aaaCTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAAt < 1:3001013/69‑1 (MQ=255)
aaaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTgg < 1:2743755/69‑1 (MQ=255)
aaaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTgg < 1:1253699/69‑1 (MQ=255)
aaaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTgg < 1:1132289/69‑1 (MQ=255)
aaaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTgg < 1:1728506/69‑1 (MQ=255)
aaaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTgg < 1:200508/69‑1 (MQ=255)
aaaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTgg < 1:2780102/69‑1 (MQ=255)
aaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCATAGGTGa < 1:1346/56‑1 (MQ=255)
aaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGa < 1:3280172/56‑1 (MQ=255)
aaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGa < 1:3200727/56‑1 (MQ=255)
aaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGa < 1:2023433/56‑1 (MQ=255)
aaTGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGa < 1:1024152/56‑1 (MQ=255)
|
ACGCCAGTAATAGCAAACCGCATACATCAAAAAACTAAATGTCACTAACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTGG > minE/1556732‑1556836
|
| 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
