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 |
2,246,389 |
T→C |
21.5% |
Y34Y (TAT→TAC) |
thiC → |
thiamin (pyrimidine moiety) biosynthesis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,246,389 | 0 | T | C | 21.5%
| 78.9
/ 15.2
| 60 | Y34Y (TAT→TAC) | thiC | thiamin (pyrimidine moiety) biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base T (19/28); new base C (5/8); total (24/36) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.18e-01 |
CGCCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTAGCCCGACGCTAATT > minE/2246323‑2246455
|
cgcCCGGGCCCAACATTTTATCGACACCCTGGATGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:354788/69‑1 (MQ=255)
cgcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:2689821/69‑1 (MQ=255)
cgcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:480319/69‑1 (MQ=255)
cgcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:2390374/69‑1 (MQ=255)
cgcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:173963/69‑1 (MQ=255)
gcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:2872772/68‑1 (MQ=255)
gcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTatat < 1:1223675/68‑1 (MQ=255)
gcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATc < 1:3094855/69‑1 (MQ=255)
gcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATc < 1:2872593/69‑1 (MQ=255)
gcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATc < 1:832325/69‑1 (MQ=255)
gcCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACCCATTTatat < 1:1453618/68‑1 (MQ=255)
cccGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATc < 1:2390640/68‑1 (MQ=255)
cccGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATc < 1:80887/68‑1 (MQ=255)
ccaggCCCAACATTTTATCGATACCCTGGAAGGCTCCGCCTTTCGCAACTCAAAACGCATTTACATCAc > 1:684427/4‑69 (MQ=255)
ccaggCCCAACATTTTATCGATACCCTGGAAGGCTCCGCCTTTCCCAACTCAAAACGCATTTACATCAc > 1:1687685/4‑69 (MQ=255)
ccaggCCCAACATTTTATCGATACCCTGGAAGGCTCCGCCTTTCCCAACTCAAAACGCATTTACATCAc > 1:3256711/4‑69 (MQ=255)
ccaggCCCAACATTTTATCGATACCCTGGAAGGCTCCGCCTTTCCCAACTCAAAACGCATTTACATCAc > 1:428138/4‑69 (MQ=255)
ccaggCCCAACATTTTATCGATACCCTGGAAGGCTCCGCCTTTCCCAACTCAAAACGCATTTACATCAc > 1:1354648/4‑69 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:997673/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:1174987/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:862267/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:428978/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:2691386/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:645550/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:162897/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:2048011/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:1883746/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:1914041/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:2003605/69‑1 (MQ=255)
cccAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:1522036/69‑1 (MQ=255)
ttATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCacacac > 1:729691/1‑65 (MQ=255)
ttATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCacacac > 1:2923148/1‑65 (MQ=255)
ttATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCacacac > 1:2004622/1‑65 (MQ=255)
ttATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCacacac > 1:1968290/1‑65 (MQ=255)
aaGGCACCGCCTTTCCCAACTCAAAACGCATTTATATc < 1:1680674/38‑1 (MQ=255)
aGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGa < 1:164012/68‑1 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:2704637/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:3154831/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:3058529/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:2871024/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:1269771/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:130638/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:2392635/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:2277425/1‑68 (MQ=255)
cACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCCCGTGCCGATg > 1:2328580/1‑67 (MQ=255)
cACCGACTTTCCCAACTCAAAACGCATTTATATCACTGGcacaca > 1:1159919/1‑45 (MQ=255)
aCCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:467066/1‑67 (MQ=255)
aCCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:3042947/1‑67 (MQ=255)
aCCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:2307237/1‑67 (MQ=255)
aCCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:2307088/1‑67 (MQ=255)
aCCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGc > 1:3201951/1‑67 (MQ=255)
cGCCTTTCCCAACTCAAAACGCATTTATATCACTGGca < 1:1476919/38‑1 (MQ=255)
gCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTgag < 1:403163/69‑1 (MQ=255)
gCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTgag < 1:26578/69‑1 (MQ=255)
gCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTgag < 1:1810265/69‑1 (MQ=255)
gCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTgag < 1:2959396/69‑1 (MQ=255)
gCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTgag < 1:254446/69‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:3430351/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:814857/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:2290563/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:718876/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:2414002/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:1088649/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:3314064/67‑1 (MQ=255)
ccTTTCCCAACTCAAAACGCATTTACATCACTGCCACACAACCCGGCGTGCGCGTGCCGATGCGTga < 1:350576/67‑1 (MQ=255)
aCTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTa < 1:2855071/69‑1 (MQ=255)
aCTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTa < 1:2048770/69‑1 (MQ=255)
aCTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTa < 1:118788/69‑1 (MQ=255)
tataTCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTAGCCCGACGCTAAtt > 1:3345218/1‑69 (MQ=255)
tataTCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTAGCCCGACGCTAAtt > 1:1091433/1‑69 (MQ=255)
tataTCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTAGCCCGACGCTAAt > 1:2302154/1‑68 (MQ=255)
tataTCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTAGCCCGACGCTAAt > 1:3174156/1‑68 (MQ=255)
|
CGCCCGGGCCCAACATTTTATCGACACCCTGGAAGGCACCGCCTTTCCCAACTCAAAACGCATTTATATCACTGGCACACACCCCGGCGTGCGCGTGCCGATGCGTGAGATCCAGCTTAGCCCGACGCTAATT > minE/2246323‑2246455
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
