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 |
1,020,048 |
T→C |
66.8% |
T165T (ACA→ACG) |
uidC ← |
predicted outer membrane porin protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,020,048 | 0 | T | C | 66.8%
| 53.2
/ 31.8
| 66 | T165T (ACA→ACG) | uidC | predicted outer membrane porin protein |
| Reads supporting (aligned to +/- strand): ref base T (8/14); new base C (15/29); total (23/43) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGC > minE/1019982‑1020113
|
acaggTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGgtg > 1:2486418/4‑68 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCTCCACAGGTCAATATTTGGCGTTaa < 1:1195260/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:74368/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1901670/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1890363/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:2001764/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:2750992/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:2964942/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1822226/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:3009187/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:460872/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1634478/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:611568/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:670095/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:744467/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:82666/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:839597/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1362679/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1340565/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:2301708/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1285253/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:1171178/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:996483/69‑1 (MQ=255)
ggTTGTTGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:2458351/69‑1 (MQ=255)
ggTTGTT‑AATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:2091030/68‑1 (MQ=255)
gttgttGAATCGGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:975180/68‑1 (MQ=255)
gttgAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGc > 1:1025357/1‑68 (MQ=255)
tgAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGccc < 1:2859776/68‑1 (MQ=255)
tgAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGccc < 1:2947389/68‑1 (MQ=255)
aGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAAc > 1:1324688/1‑68 (MQ=255)
cATAAAAATACTCGTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTaa < 1:3160055/53‑1 (MQ=255)
cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt > 1:2810701/1‑69 (MQ=255)
cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt > 1:57442/1‑69 (MQ=255)
cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt > 1:1045692/1‑69 (MQ=255)
cATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAAt > 1:1721226/1‑69 (MQ=255)
cTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCa > 1:839718/1‑68 (MQ=255)
cTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCa > 1:2366328/1‑68 (MQ=255)
gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa < 1:2445616/55‑1 (MQ=255)
gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa < 1:184018/55‑1 (MQ=255)
gTGAACGCCACATTCCCCACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTaa < 1:1859870/55‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:1565901/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:109325/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:915501/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:816/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:1509602/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:704601/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:580172/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:1747893/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:2685249/69‑1 (MQ=255)
ttCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATg < 1:1824142/69‑1 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCt > 1:3366341/1‑48 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:1784359/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:2038991/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:1292686/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:962575/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:2417925/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:1503713/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:1554046/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:3146949/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:686073/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:2038235/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:1613192/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:2245930/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTa > 1:487356/1‑69 (MQ=255)
ccccACAGGTCAATATTTGGCGTTAAAGCCCAACAACCTAATGCTACTTCAGAAACTGTCgg > 1:1503286/1‑62 (MQ=255)
tGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTgccagc < 1:880921/69‑1 (MQ=255)
tGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTgccagc < 1:1757285/69‑1 (MQ=255)
|
ACCGGTTGTTGAATCAGTCCATAAAAATACTCGTGAACGCCACATTCCCCACAGATCAATATTTGGTGTTAAAGCCCAATAACCTAATGCTCCTTCAGAAACTGTCGGTAATGTACGTTGCGAACTGCCAGC > minE/1019982‑1020113
|
| 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
