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 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,485,005 |
C→T |
19.1% |
D279N (GAT→AAT) |
menF ← |
isochorismate synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,485,005 | 0 | C | T | 19.1%
| 157.1
/ 30.0
| 68 | D279N (GAT→AAT) | menF | isochorismate synthase 2 |
| Reads supporting (aligned to +/- strand): ref base C (26/28); new base T (10/3); total (37/31) |
| Fisher's exact test for biased strand distribution p-value = 7.25e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.72e-01 |
GTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTG > minE/1484941‑1485067
|
gTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGc < 1:2813800/71‑1 (MQ=255)
tATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGc < 1:3893579/70‑1 (MQ=255)
tCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCa > 1:3725457/1‑70 (MQ=255)
ggCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCAt > 1:2958438/1‑69 (MQ=255)
ccTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGc < 1:4338/71‑1 (MQ=255)
gTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc < 1:2412594/58‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCa < 1:3960316/69‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAct < 1:1114144/71‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc < 1:834083/70‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc < 1:607130/70‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc < 1:46971/70‑1 (MQ=255)
aaTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCctct < 1:1899510/70‑1 (MQ=255)
aaTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa > 1:4117606/1‑68 (MQ=255)
aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc < 1:1331731/70‑1 (MQ=255)
aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc < 1:1272149/70‑1 (MQ=255)
aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc < 1:979677/70‑1 (MQ=255)
cGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACtctc > 1:3220371/1‑70 (MQ=255)
cGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTcc > 1:3851378/1‑71 (MQ=255)
cGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTcc > 1:693560/1‑71 (MQ=255)
gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTtattat > 1:1076668/1‑51 (MQ=255)
gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCt < 1:985012/71‑1 (MQ=255)
gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCt < 1:3209623/71‑1 (MQ=255)
ttGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTa < 1:2014948/71‑1 (MQ=255)
ttGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTa < 1:13717/71‑1 (MQ=255)
cAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAActg < 1:1667682/71‑1 (MQ=255)
aGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAActgc > 1:1843356/1‑71 (MQ=255)
tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc > 1:1305984/1‑43 (MQ=255)
tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc > 1:1487374/1‑43 (MQ=255)
tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc > 1:2906208/1‑43 (MQ=255)
tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc > 1:3799944/1‑43 (MQ=255)
tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTattatc > 1:3718630/1‑43 (MQ=255)
tatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACtgctgc < 1:2114226/71‑1 (MQ=255)
atCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcg > 1:1921220/1‑71 (MQ=255)
atCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcg > 1:837079/1‑71 (MQ=255)
atCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcg > 1:3933409/1‑71 (MQ=255)
tCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc < 1:888014/56‑1 (MQ=255)
tCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTgcgc > 1:1663723/1‑71 (MQ=255)
cTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAActgct > 1:4022172/1‑66 (MQ=255)
ccaccaccaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGc > 1:1591741/1‑71 (MQ=255)
caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa > 1:22547/1‑54 (MQ=255)
caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa > 1:1714269/1‑54 (MQ=255)
caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa > 1:3892060/1‑54 (MQ=255)
caccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTaa > 1:3701132/1‑54 (MQ=255)
accaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatc < 1:3434081/71‑1 (MQ=255)
accaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatc < 1:3953927/71‑1 (MQ=255)
accaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCCCCTGCTTatc < 1:50951/71‑1 (MQ=255)
caGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat < 1:1254054/71‑1 (MQ=255)
aGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAg > 1:916949/1‑38 (MQ=255)
aGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAg > 1:2705214/1‑38 (MQ=255)
aGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat > 1:2083456/1‑70 (MQ=255)
gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat > 1:3356049/1‑69 (MQ=255)
gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat > 1:668980/1‑69 (MQ=255)
gCATGTTCTCGAGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat > 1:736725/1‑69 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:2122027/1‑70 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATGATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:3837205/1‑70 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGcc > 1:162070/1‑57 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:622851/1‑70 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:4103686/1‑70 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:3585743/1‑70 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:3966310/1‑70 (MQ=255)
aTGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAg > 1:1548474/1‑70 (MQ=255)
tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa < 1:3204500/62‑1 (MQ=255)
tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa < 1:1057591/62‑1 (MQ=255)
tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa < 1:3209426/62‑1 (MQ=255)
tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa < 1:3904854/62‑1 (MQ=255)
tGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa < 1:3933011/62‑1 (MQ=255)
ctcGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGattat > 1:272038/1‑71 (MQ=255)
ctcGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGattat > 1:1136619/1‑71 (MQ=255)
ctcGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGattat > 1:4244483/1‑71 (MQ=255)
gcTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc > 1:714648/1‑70 (MQ=255)
gcTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc > 1:2593569/1‑70 (MQ=255)
gcTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc > 1:1344186/1‑70 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg < 1:1910918/71‑1 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg < 1:263385/71‑1 (MQ=255)
gTTTTTAACATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg < 1:3786878/71‑1 (MQ=255)
|
GTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTG > minE/1484941‑1485067
|
| 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
