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 |
2,294,089 |
C→A |
19.2% |
intergenic (+116/‑159) |
gldA → / → yijF |
glycerol dehydrogenase, NAD/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,294,089 | 0 | C | A | 19.2%
| 139.4
/ 14.7
| 52 | intergenic (+116/‑159) | gldA/yijF | glycerol dehydrogenase, NAD/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (18/24); new base A (8/2); total (26/26) |
| Fisher's exact test for biased strand distribution p-value = 7.51e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
ATGCGCTACGCTTATCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACGTTGTTCAGGAATT > minE/2294024‑2294159
|
aTGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGAt > 1:2431973/1‑70 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGAt > 1:1089080/1‑70 (MQ=255)
tACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAg > 1:1461516/1‑67 (MQ=255)
tACGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGATTTTGTAGGCAGGATAAg > 1:2979552/1‑67 (MQ=14)
cGCTTATCAGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTc < 1:1533679/71‑1 (MQ=255)
cGCTTATCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGtt > 1:293116/1‑70 (MQ=255)
cGCTTATCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGtt > 1:1554278/1‑70 (MQ=255)
cGCTTATCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGt < 1:3173641/69‑1 (MQ=255)
ttATCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCg < 1:321679/65‑1 (MQ=255)
ttATCAGGCCTAAGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACt > 1:2043816/1‑71 (MQ=255)
tCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTcc < 1:1103155/70‑1 (MQ=255)
tCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCg < 1:1062469/71‑1 (MQ=255)
aGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGc > 1:414829/1‑59 (MQ=17)
aGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCa > 1:2116405/1‑71 (MQ=14)
aGGCCTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCa > 1:2111750/1‑71 (MQ=14)
aGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCAc > 1:1103871/1‑65 (MQ=255)
aGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCa > 1:972255/1‑71 (MQ=255)
ggCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCAt < 1:3878604/71‑1 (MQ=255)
gCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATc < 1:2697775/71‑1 (MQ=255)
ccTACGCCATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATcc > 1:560551/1‑71 (MQ=11)
aCGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCgg > 1:3306699/1‑70 (MQ=255)
cGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCgg < 1:3844082/69‑1 (MQ=255)
cAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATa < 1:3845639/46‑1 (MQ=255)
cAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATcc > 1:2099575/1‑65 (MQ=255)
aaTCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATa < 1:769919/45‑1 (MQ=255)
aaTCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATa < 1:1773593/45‑1 (MQ=255)
aTCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCActct < 1:818982/71‑1 (MQ=255)
aTCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCActct < 1:976881/71‑1 (MQ=255)
tGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGAt < 1:1529479/38‑1 (MQ=40)
aaTATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATcc > 1:1436048/1‑55 (MQ=255)
atatatTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGc > 1:1873816/1‑39 (MQ=40)
tatatTGAATTTGCGTGCTTTTGTAGGCAGGATAAGGCg < 1:3311391/39‑1 (MQ=255)
tatTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAAt < 1:2116238/70‑1 (MQ=255)
tatTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAAt < 1:1429239/70‑1 (MQ=255)
tGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTg > 1:1637148/1‑70 (MQ=255)
gAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGa < 1:2815262/70‑1 (MQ=255)
gAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGa < 1:1566549/70‑1 (MQ=255)
aaTTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGaa < 1:1661105/70‑1 (MQ=255)
tttGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGa < 1:3630816/67‑1 (MQ=255)
tGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTcc > 1:2398074/1‑71 (MQ=255)
tGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTc < 1:957084/70‑1 (MQ=255)
gCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTcc > 1:994397/1‑70 (MQ=255)
gCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTcc > 1:2090238/1‑70 (MQ=255)
cGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTccc < 1:2630861/70‑1 (MQ=255)
gCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACgt > 1:649805/1‑71 (MQ=255)
ttttGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGa > 1:2168527/1‑58 (MQ=255)
ttGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTg > 1:456866/1‑55 (MQ=255)
ttGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGaaa > 1:1024017/1‑58 (MQ=255)
tGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACCCCCACgttgtt < 1:211526/70‑1 (MQ=255)
gTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACgttgtt > 1:1767428/1‑69 (MQ=255)
gTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACGTTGTTc < 1:889807/70‑1 (MQ=255)
gCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACGTTGTTCAGGaa < 1:853623/71‑1 (MQ=255)
cGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTg < 1:2465430/47‑1 (MQ=255)
cGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACGTTGTTCAGGAAtt < 1:3101121/71‑1 (MQ=255)
|
ATGCGCTACGCTTATCAGGCCTACGCAATCTCTGCAATATATTGAATTTGCGTGCTTTTGTAGGCCGGATAAGGCGTTCACTCCGCATCCGGCACTCTGTGCCAGTAATCTGAAACTCCCACGTTGTTCAGGAATT > minE/2294024‑2294159
|
| 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
