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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,439,444 |
G→A |
15.1% |
Y286Y (TAC→TAT) |
ompC ← |
outer membrane porin protein C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,439,444 | 0 | G | A | 15.1%
| 267.7
/ 30.5
| 99 | Y286Y (TAC→TAT) | ompC | outer membrane porin protein C |
| Reads supporting (aligned to +/- strand): ref base G (53/31); new base A (5/10); total (58/41) |
| Fisher's exact test for biased strand distribution p-value = 4.54e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 |
Only 100 of 104 total aligned reads displayed.
CCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCGTTGT > minE/1439376‑1439514
|
ccACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGt < 1:3153461/70‑1 (MQ=255)
ccACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTa > 1:1158037/1‑71 (MQ=255)
aCGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:224211/71‑1 (MQ=255)
aCGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:2695219/71‑1 (MQ=255)
aCGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt > 1:1587104/1‑71 (MQ=255)
gACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt > 1:1391016/1‑69 (MQ=255)
gACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGa < 1:1939108/71‑1 (MQ=255)
aGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAAc < 1:3687990/71‑1 (MQ=255)
gTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTa > 1:1830990/1‑60 (MQ=255)
gTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAg > 1:1384207/1‑71 (MQ=255)
tttttACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:3264392/61‑1 (MQ=255)
ttttACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:2586165/60‑1 (MQ=255)
tttACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGa > 1:2519782/1‑61 (MQ=255)
tttACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCtt > 1:3609629/1‑71 (MQ=255)
ttacctgcagtctaaaggtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:3106701‑M2/37‑1 (MQ=255)
acctgcagtctaaaggtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg > 1:2292183‑M2/20‑70 (MQ=255)
aCCTTTAGATTGCAGGTAAGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTca < 1:1219581/70‑2 (MQ=18)
ACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg > 1:860289‑M1/1‑70 (MQ=255)
ACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg > 1:3243455‑M1/1‑70 (MQ=255)
ccTTTAGATTGCAGGTAAGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCaaa < 1:3452313/71‑1 (MQ=16)
CCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg > 1:3684646‑M1/1‑69 (MQ=255)
cTTTAGATTGCAGGTAAGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCAAAg > 1:91448/1‑71 (MQ=16)
ttAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGc > 1:837870/1‑56 (MQ=255)
ttAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGtt > 1:908807/1‑71 (MQ=255)
ttAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGtt > 1:955654/1‑71 (MQ=255)
ttAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGtt > 1:1497516/1‑71 (MQ=255)
tAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTc > 1:3518907/1‑71 (MQ=255)
tAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTc > 1:193162/1‑71 (MQ=255)
tAGACTGCAGCTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTc > 1:1662945/1‑71 (MQ=255)
gACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCtg < 1:2175608/71‑1 (MQ=255)
cTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCtgt > 1:3358854/1‑70 (MQ=255)
tGCAGGTAAGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCAAAGTTTtggg > 1:3539664/1‑68 (MQ=12)
cAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCtt > 1:3622126/1‑71 (MQ=255)
cAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCtt > 1:1470464/1‑71 (MQ=255)
cAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCtt > 1:434528/1‑71 (MQ=255)
cAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCtt > 1:465393/1‑71 (MQ=255)
ggtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACa < 1:3770869‑M2/45‑1 (MQ=255)
ggtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTg < 1:1808799‑M2/66‑1 (MQ=255)
ggtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTg > 1:2432084‑M2/6‑71 (MQ=255)
ggTAAGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTg < 1:671175/71‑1 (MQ=12)
gtaaGCCATGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGt > 1:2553311‑M2/5‑71 (MQ=255)
gtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGt > 1:3472081‑M2/5‑71 (MQ=255)
gtaaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGt > 1:1647389‑M2/5‑71 (MQ=255)
taaGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGtt < 1:3317240‑M2/68‑1 (MQ=255)
aaGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGt > 1:1591140/1‑69 (MQ=12)
aaGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGt > 1:3777063/1‑69 (MQ=12)
aaGCGATGGACGGGCGCAGGCCAAAGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGt > 1:3566872/1‑69 (MQ=12)
aGCCAGGGCCGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTc < 1:1460458‑M2/69‑1 (MQ=255)
aGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTc < 1:3164980‑M2/69‑1 (MQ=255)
ccAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg < 1:1980543/50‑1 (MQ=255)
ccAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg < 1:302289/50‑1 (MQ=255)
aGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGccc > 1:2357432/1‑70 (MQ=255)
aGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGc > 1:1691457/1‑68 (MQ=255)
gggACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCg > 1:3157843/1‑66 (MQ=255)
gggACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCaa > 1:2678961/1‑71 (MQ=255)
acggacgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAAccc < 1:3771531/71‑1 (MQ=255)
cggacgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCg < 1:3892933/43‑1 (MQ=255)
cggacgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAAccc < 1:79359/70‑1 (MQ=255)
ggacgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCtg < 1:1479414/50‑1 (MQ=255)
acgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAgg > 1:1629976/1‑70 (MQ=255)
acgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAgg > 1:3512753/1‑70 (MQ=255)
acgCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAgg > 1:3947181/1‑70 (MQ=255)
gCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGcc > 1:2047331/1‑59 (MQ=255)
gCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGaa > 1:3477011/1‑71 (MQ=255)
cAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAAc < 1:2047919/71‑1 (MQ=255)
cAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAAc < 1:1950751/71‑1 (MQ=255)
aGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTc < 1:3145725/54‑1 (MQ=255)
aGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAAcc > 1:2904924/1‑71 (MQ=255)
gACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCt < 1:1629197/71‑1 (MQ=255)
aCCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTa > 1:3220294/1‑71 (MQ=255)
aCCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTa > 1:2061859/1‑71 (MQ=255)
aCCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTATTCGCCCAACCCAGGGAACCTa > 1:1071219/1‑71 (MQ=255)
ccGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCg > 1:2651472/1‑52 (MQ=255)
ccGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGaa > 1:1765266/1‑66 (MQ=255)
cGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTc < 1:589999/50‑1 (MQ=255)
cGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTa < 1:3089718/69‑1 (MQ=255)
gAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTAcgc < 1:1510194/71‑1 (MQ=255)
aaaGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGtttt < 1:898203/44‑1 (MQ=16)
aaaGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGtttt < 1:241357/44‑1 (MQ=16)
aaaGTCGAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGt < 1:134462/46‑1 (MQ=19)
aaGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCttt > 1:3850996/1‑44 (MQ=255)
aaGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCttt > 1:2652899/1‑44 (MQ=255)
aaGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGc > 1:3914051/1‑50 (MQ=255)
aaGTCGAACTGATACTGAGCAACAACTTCAAAGTTTtg < 1:435019/38‑1 (MQ=21)
gTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAg < 1:3332638/71‑1 (MQ=255)
tCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTg < 1:3077257/42‑1 (MQ=255)
cGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGtt > 1:1787420/1‑71 (MQ=255)
gAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGTTAGcga < 1:3387140/47‑3 (MQ=12)
gAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGTTAGcg < 1:503352/46‑2 (MQ=12)
gAACTGATACTGAGCAACAACTTCAAAGTTTTGGGTTTTGTTAGcg < 1:1436413/46‑2 (MQ=12)
aCTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTg < 1:1482405/38‑1 (MQ=255)
aCTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCg > 1:520757/1‑71 (MQ=255)
aCTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCg > 1:2455338/1‑71 (MQ=255)
aCTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCg > 1:338337/1‑71 (MQ=255)
aCTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCAAGGGa > 1:2513961/1‑55 (MQ=255)
ggTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGccc > 1:3730668/1‑42 (MQ=255)
ggTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGccc > 1:2243854/1‑42 (MQ=255)
ggTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCa < 1:3922949/43‑1 (MQ=255)
gTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCGTTGt < 1:2675591/71‑1 (MQ=255)
gTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCGTTGt < 1:1773293/71‑1 (MQ=255)
|
CCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTTCGCCCAACCCAGGGAACCTACGCGAGTTGCGTTGT > minE/1439376‑1439514
|
| 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
