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 |
484,650 |
G→A |
66.1% |
V152V (GTG→GTA) |
tolB → |
periplasmic protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 484,650 | 0 | G | A | 66.1%
| 34.7
/ 27.9
| 53 | V152V (GTG→GTA) | tolB | periplasmic protein |
| Reads supporting (aligned to +/- strand): ref base G (16/2); new base A (21/14); total (37/16) |
| Fisher's exact test for biased strand distribution p-value = 5.57e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 |
TCGTACAAAGTGAACAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAC > minE/484591‑484716
|
tCGTACAAAGTGAACAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGATGAAGTGTTTGaaaaa < 1:2385764/69‑1 (MQ=255)
aCAAAGTGAACAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTg < 1:243013/68‑1 (MQ=255)
aaCAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTAt > 1:101264/1‑68 (MQ=255)
aaCAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTAt > 1:2187822/1‑68 (MQ=255)
aaCAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTAt > 1:2328061/1‑68 (MQ=255)
aaCAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTAt > 1:2941738/1‑68 (MQ=255)
aaCAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTAt > 1:1783469/1‑68 (MQ=255)
aaCAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTAt > 1:2968138/1‑68 (MQ=255)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACt > 1:2183805/1‑44 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:3024568/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:3038707/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:3164861/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:3356674/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:2523493/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:251852/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:824750/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:901362/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:918482/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:11029/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:1651069/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:1900007/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCggt > 1:1488387/1‑50 (MQ=38)
cGTTATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCgg > 1:3050965/1‑50 (MQ=39)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2556490/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2992004/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2959420/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:426881/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2602504/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2549774/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:1842731/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:252342/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2429957/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2202629/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:2151363/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGGTCCGTa < 1:715168/68‑1 (MQ=255)
ttATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGGTCCGTa < 1:1888/68‑1 (MQ=255)
tATGCTGGTCATACCGCCAGTGACGAAGTATTTGAAAAACTGACCGGTATTAAAGGTGCGTTCCGTa < 1:1675098/67‑1 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTa > 1:1636327/1‑69 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTa > 1:1407376/1‑69 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTa > 1:1706926/1‑69 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTa > 1:2977244/1‑69 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTa > 1:2295828/1‑69 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTa > 1:1702821/1‑69 (MQ=255)
cTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTAGTa > 1:926583/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCTGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:2619374/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:3045102/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:3303067/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:686047/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:701161/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:827444/1‑69 (MQ=255)
aCCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTAc > 1:1989411/1‑69 (MQ=255)
gatgaAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAg > 1:2586897/1‑69 (MQ=255)
gaAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGAcc > 1:2019118/1‑69 (MQ=255)
gtgtTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAc > 1:1831973/1‑69 (MQ=255)
gtgtTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAc > 1:342162/1‑69 (MQ=255)
gtgtTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAc > 1:588524/1‑69 (MQ=255)
gtgtTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAc > 1:1893786/1‑69 (MQ=255)
gtgtTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAc > 1:1415487/1‑69 (MQ=255)
|
TCGTACAAAGTGAACAAGCAGTGGCTGCGTTATGCTGGTCATACCGCCAGTGATGAAGTGTTTGAAAAACTGACCGGCATTAAAGGTGCGTTCCGTACTCGTATTGCCTACGTTGTTCAGACCAAC > minE/484591‑484716
|
| 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
