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 |
1,357,250 |
C→T |
54.0% |
L624L (TTG→TTA) |
yehB ← |
predicted outer membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,357,250 | 0 | C | T | 54.0%
| 2.9
/ 54.2
| 63 | L624L (TTG→TTA) | yehB | predicted outer membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (9/20); new base T (18/16); total (27/36) |
| Fisher's exact test for biased strand distribution p-value = 1.25e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTG > minE/1357185‑1357318
|
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:1030576/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:679521/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:2308126/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:2858974/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:2860725/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:399022/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:3311575/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:1069534/67‑1 (MQ=255)
gCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCAAGGTCa < 1:1784203/67‑1 (MQ=255)
ccTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCa < 1:248033/66‑1 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCg > 1:181710/1‑60 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCa > 1:2088630/1‑65 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTg > 1:3095891/1‑69 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTg > 1:2974268/1‑69 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTg > 1:1089/1‑69 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTg > 1:205214/1‑69 (MQ=255)
tACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTg > 1:1905552/1‑69 (MQ=255)
tACTCGACTGACTATAACTGCCATTAACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTg > 1:3323496/1‑69 (MQ=255)
cGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGt < 1:180741/69‑1 (MQ=255)
cGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGt < 1:1842966/69‑1 (MQ=255)
cACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTtgat > 1:900011/1‑68 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCa > 1:1199415/1‑51 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCAttt > 1:717707/1‑54 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTccc > 1:2948134/1‑57 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:2465705/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:1399569/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:2446028/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:413662/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:252903/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:48261/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:2554657/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:2710474/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:1385620/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:521719/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:1701008/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTCCCt > 1:11852/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTAATTTCCCt > 1:2885759/1‑58 (MQ=255)
aCTGTCGCAACCGGCGCGTTCCAGGATAAATTCGccc > 1:2079052/1‑37 (MQ=37)
aCTGTCGCAACCGGCGCGTTCAAGGTTAAATTCGCCCCAGATGTCGtt > 1:2971458/1‑48 (MQ=38)
aaCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:2459441/69‑1 (MQ=255)
aaCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:2413466/69‑1 (MQ=255)
aaCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:271559/69‑1 (MQ=255)
aaCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:2112789/69‑1 (MQ=255)
aaCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:1621468/69‑1 (MQ=255)
aaCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:1735151/69‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCAtttgc < 1:1480832/47‑3 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:403613/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:3345802/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:326721/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:1811472/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:734276/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:2513559/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:2352499/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:2194490/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:2114634/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:2031101/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:49579/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTTAAATTCGCACCAGCTGTCGTTTCATTTcc < 1:973800/47‑1 (MQ=255)
aCCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGtt < 1:2326206/68‑1 (MQ=255)
ccGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:831526/46‑1 (MQ=255)
ccGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:883665/46‑1 (MQ=255)
cGGCGCGTTCCAGGTTAAATTCGCCCCAGCTGTCGTTTCATTTcc < 1:2445752/45‑1 (MQ=255)
ggTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGa < 1:1495713/68‑1 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACt > 1:127662/1‑68 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg < 1:3122348/69‑1 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg > 1:3408344/1‑69 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg > 1:3114177/1‑69 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg < 1:3089455/69‑1 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg < 1:1859435/69‑1 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg < 1:1680940/69‑1 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg < 1:1364666/69‑1 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg > 1:123746/1‑69 (MQ=255)
cAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTg > 1:1055081/1‑69 (MQ=255)
|
GCCTGTCGATAAGTACTCGACTGACTATAACTGCCATTCACTGTCGCAACCGGCGCGTTCCAGGTCAAATTCGCCCCAGCTGTCGTTTCATTTCCCTGATGTTGATGACTCAGGTTGACACCATAATTGAACTG > minE/1357185‑1357318
|
| 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
