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 |
312,696 |
G→A |
20.4% |
D59D (GAC→GAT) |
acrB ← |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 312,696 | 0 | G | A | 20.4%
| 188.4
/ 40.4
| 88 | D59D (GAC→GAT) | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base G (27/43); new base A (11/7); total (38/50) |
| Fisher's exact test for biased strand distribution p-value = 1.11e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01 |
ACTGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCGT > minE/312627‑312764
|
aCTGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCgtg < 1:1065346/70‑1 (MQ=255)
aCTGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCgtg < 1:1075688/70‑1 (MQ=255)
aCTGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCgtg < 1:3068805/70‑1 (MQ=255)
tGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTcc > 1:1747006/1‑71 (MQ=255)
tGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTcc > 1:2684014/1‑71 (MQ=255)
ttAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTcc < 1:3427591/69‑1 (MQ=255)
ttAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTg < 1:2326700/71‑1 (MQ=255)
ttAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTg < 1:2407123/71‑1 (MQ=255)
ttAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTg > 1:1333341/1‑71 (MQ=255)
gtggagGACATATACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTg < 1:1630433/68‑1 (MQ=25)
gtggagGACATATACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTg > 1:3111717/4‑71 (MQ=25)
gtggagGACATATACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTg < 1:512134/68‑1 (MQ=25)
tAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTg > 1:290465/1‑70 (MQ=255)
agagGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGc < 1:2878758/70‑1 (MQ=255)
agagGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCa > 1:541248/1‑71 (MQ=255)
agagGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCa > 1:999350/1‑71 (MQ=255)
agGACATATACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCAcg > 1:3447145/1‑70 (MQ=255)
ggACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTg < 1:1190008/71‑1 (MQ=255)
cATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGttt < 1:248404/71‑1 (MQ=255)
cATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGttt < 1:1026371/71‑1 (MQ=255)
cATGTACATCAGCTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGttt < 1:1211857/71‑1 (MQ=255)
tGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTc < 1:1535085/71‑1 (MQ=255)
tACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTc > 1:612396/1‑69 (MQ=255)
tACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTc > 1:1247704/1‑69 (MQ=255)
tACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCg > 1:352436/1‑70 (MQ=255)
tACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGc < 1:1873206/71‑1 (MQ=255)
aCATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCa > 1:2709462/1‑71 (MQ=255)
cATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCTCAt < 1:1813843/71‑1 (MQ=255)
cATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCAt < 1:1594504/71‑1 (MQ=255)
cATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCAt < 1:3837007/71‑1 (MQ=255)
cATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCAt < 1:265665/71‑1 (MQ=255)
cATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCAt < 1:514134/71‑1 (MQ=255)
cATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCAt < 1:3274708/71‑1 (MQ=255)
aTCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCAt > 1:964414/1‑70 (MQ=255)
aTCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc < 1:272665/71‑1 (MQ=255)
aTCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc < 1:3355219/71‑1 (MQ=255)
aTCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc < 1:1739761/71‑1 (MQ=255)
aTCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCAt > 1:1037871/1‑70 (MQ=37)
tCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCa < 1:53633/71‑1 (MQ=255)
aGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGc > 1:2659004/1‑65 (MQ=255)
aGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGTATCAg < 1:480624/70‑1 (MQ=255)
aGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAg < 1:405278/70‑1 (MQ=255)
aGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAgc > 1:3362124/1‑71 (MQ=37)
ttATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc > 1:2431728/1‑65 (MQ=255)
tATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc > 1:1697515/1‑64 (MQ=255)
tATCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAGCGccc > 1:714867/1‑70 (MQ=255)
aTCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTc < 1:1077446/58‑1 (MQ=255)
tCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCAcgg < 1:2761090/52‑3 (MQ=37)
tCGATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCAcgg < 1:1481597/52‑3 (MQ=37)
cGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCgggg > 1:2923637/1‑71 (MQ=255)
cGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCgggg > 1:1807409/1‑71 (MQ=255)
gATACCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAGCGCCcgga < 1:3615062/70‑2 (MQ=255)
aTACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCg < 1:2667872/66‑1 (MQ=255)
aTACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCg < 1:24974/66‑1 (MQ=255)
aTACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTa < 1:858137/71‑1 (MQ=255)
aCCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTc > 1:2316299/1‑39 (MQ=255)
aCCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTc > 1:1137373/1‑39 (MQ=255)
aCCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCAcg > 1:588285/1‑45 (MQ=37)
aCCGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCAcg > 1:1740611/1‑45 (MQ=37)
ccGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTagga < 1:1470941/71‑1 (MQ=255)
ccGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCa > 1:893231/1‑57 (MQ=255)
ccGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCa > 1:683653/1‑57 (MQ=255)
ccGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAGCGCCCGGATagtt > 1:3706071/1‑69 (MQ=25)
cGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAGCGCCCGGATagttt < 1:1412321/71‑4 (MQ=255)
cGTTCATATTCTGTTCGATAACCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAGCGCCCGGATagttt < 1:173351/71‑4 (MQ=255)
gTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc < 1:3919259/54‑1 (MQ=255)
cATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc > 1:1537787/1‑51 (MQ=255)
atatTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGcc < 1:1086841/56‑1 (MQ=255)
atTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATc < 1:43547/48‑1 (MQ=255)
ttCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGAt < 1:3928209/71‑1 (MQ=255)
cTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGtttt > 1:346902/1‑39 (MQ=255)
cTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGtttt > 1:575913/1‑39 (MQ=255)
cTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCTGGGTAGGAGGCGGAGATCg > 1:2437973/1‑71 (MQ=255)
ttCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGcc < 1:1009101/48‑1 (MQ=255)
ttCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGcc < 1:1310219/48‑1 (MQ=255)
ttCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCg < 1:2771027/68‑1 (MQ=255)
ttCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGt < 1:315028/69‑1 (MQ=255)
tCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTAc > 1:3030298/1‑71 (MQ=255)
cGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGTGCCGGGGTAGGAGGCGGAGATCGTTAc > 1:1280558/1‑70 (MQ=255)
cGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACt > 1:348681/1‑71 (MQ=255)
aTAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTagga < 1:3662500/53‑1 (MQ=255)
aTAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGc < 1:3503577/71‑1 (MQ=255)
aaCCTGCGTCACCGTATCCTGCACGGTCTGCGCATCAGCGCCcggat > 1:1763248/1‑45 (MQ=16)
cTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCcggcg > 1:3112881/1‑71 (MQ=255)
tgtCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCcggcgg < 1:56683/69‑1 (MQ=255)
tgtCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGt < 1:163203/70‑1 (MQ=255)
tgtCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGt < 1:575948/70‑1 (MQ=255)
gtCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGt < 1:1452694/56‑1 (MQ=255)
aCCGTGTCCTGCACTGTTTTCGCATCAGCGCCgggg > 1:1440289/1‑36 (MQ=255)
cGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCg < 1:3818560/71‑1 (MQ=255)
cGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCg < 1:386248/71‑1 (MQ=255)
gtgtCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCGt < 1:3062016/71‑1 (MQ=255)
gtgtCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCGt < 1:3424427/71‑1 (MQ=255)
|
ACTGTTAGAGGACATGTACATCAGGTTATCGATACCGTTCATATTCTGTTCGATAACCTGTGTCACCGTGTCCTGCACTGTTTTCGCATCAGCGCCGGGGTAGGAGGCGGAGATCGTTACTGCCGGCGGTGCAATCGT > minE/312627‑312764
|
| 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
