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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
464,884:1 |
+T |
24.1% |
intergenic (+24/‑277) |
sdhB → / → sucA |
succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamin‑requiring |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 464,884 | 1 | . | T | 24.1%
| 122.0
/ 65.4
| 58 | intergenic (+24/‑277) | sdhB/sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamin‑requiring |
| Reads supporting (aligned to +/- strand): ref base . (31/13); new base T (9/5); total (40/18) |
| Fisher's exact test for biased strand distribution p-value = 7.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGCCATCGGCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTCATTACCCGT > minE/464814‑464954
|
gcgcCATCGGCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCa < 1:5465554/71‑1 (MQ=255)
gcCATCGGCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑g > 1:624876/1‑71 (MQ=255)
aTCGGCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGt > 1:1090347/1‑71 (MQ=255)
aTCGGCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGt > 1:35157/1‑71 (MQ=255)
ggCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCg > 1:4829995/1‑70 (MQ=255)
ggCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGc < 1:1246320/71‑1 (MQ=255)
atatCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCa < 1:3049843/71‑1 (MQ=255)
tatCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAg > 1:5031890/1‑71 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCa‑a > 1:1826767/1‑57 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCa‑a > 1:324804/1‑57 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑g > 1:367953/1‑58 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑g > 1:5551587/1‑58 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑g > 1:440743/1‑58 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑g > 1:3356972/1‑58 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCAt > 1:4153199/1‑66 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGc < 1:5116807/71‑1 (MQ=255)
tCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGc < 1:4598662/71‑1 (MQ=255)
cAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGc > 1:2353200/1‑70 (MQ=255)
aGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAAc > 1:1794064/1‑71 (MQ=255)
aGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAAc > 1:799971/1‑71 (MQ=255)
gATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAg > 1:4378387/1‑70 (MQ=255)
aTGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAAc > 1:2290297/1‑66 (MQ=255)
aTGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAAc > 1:5328296/1‑66 (MQ=255)
aTGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAAc > 1:1624072/1‑66 (MQ=255)
tgttgtTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGc > 1:5400891/1‑71 (MQ=255)
gttgttGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGcc > 1:2855310/1‑71 (MQ=255)
ttgttgCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTg < 1:1834866/68‑1 (MQ=255)
gttgCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCg > 1:1339669/1‑50 (MQ=255)
gttgCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCg > 1:777925/1‑50 (MQ=255)
tacacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCa < 1:192668‑M1/27‑1 (MQ=255)
tacacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTc > 1:1920950‑M1/14‑47 (MQ=255)
tacacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTc > 1:4022236‑M1/14‑47 (MQ=255)
tacacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTc > 1:373375‑M1/14‑47 (MQ=255)
tacacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTc > 1:5000250‑M1/14‑47 (MQ=255)
gCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGc > 1:2531986/1‑48 (MQ=255)
gCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGc > 1:3950061/1‑48 (MQ=255)
gCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGc > 1:1913771/1‑48 (MQ=255)
gCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGc > 1:1694434/1‑48 (MQ=255)
cacttcgcccgTAAGCCGTAGGCCTGATAAGACGCGCA‑AAGCGTCGCAt < 1:3447958‑M1/38‑1 (MQ=255)
cacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc < 1:5248528‑M1/36‑1 (MQ=255)
cacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc < 1:2213374‑M1/36‑1 (MQ=255)
cacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc < 1:5409598‑M1/36‑1 (MQ=255)
cacttcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGCAt < 1:4947273‑M1/38‑1 (MQ=255)
cttcgcccaTAAACCGTAGGACTGATAAGACGCGCATA‑GCGTCGCATCAGGCa > 1:2507995‑M1/10‑53 (MQ=255)
tcgcccaTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGCAt < 1:309600‑M1/38‑1 (MQ=255)
tAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTg < 1:3840306/71‑1 (MQ=255)
tAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTg < 1:3085767/71‑1 (MQ=255)
cgcccgTAAGCCGTAGGCCTGATAAGACGCGCA‑AAGCGTCGCAt < 1:276795‑M1/38‑1 (MQ=255)
aTGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGaa < 1:2752619/71‑1 (MQ=255)
aTGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGaa > 1:4074436/1‑71 (MQ=255)
aTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc > 1:98135‑M1/2‑37 (MQ=255)
aTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc > 1:2218124‑M1/2‑37 (MQ=255)
aTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc > 1:951124‑M1/2‑37 (MQ=255)
aTAAACCGTAGGCCTGATAAGACGCGCATA‑GCGTCGc > 1:3048109‑M1/2‑37 (MQ=255)
ccGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATc < 1:2056247/71‑1 (MQ=255)
aTAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCGTTATCCGGCCTACAAg > 1:5401865/1‑71 (MQ=255)
aTAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACa < 1:4838075/69‑1 (MQ=255)
aTAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAg > 1:4453097/1‑71 (MQ=255)
aTAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAg > 1:351885/1‑71 (MQ=255)
gACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTCAt < 1:4442509/71‑1 (MQ=255)
aCGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTCAt > 1:1394081/1‑70 (MQ=255)
aCGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTCAt > 1:884615/1‑70 (MQ=255)
a‑a‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCgg > 1:4186831/1‑52 (MQ=255)
a‑a‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTCATTACCCGt < 1:3415362/71‑1 (MQ=255)
|
GCGCCATCGGCCATATCAAGTCGATGTTGTTGCAACGTAATGCGTAAACCGTAGGCCTGATAAGACGCGCA‑A‑GCGTCGCATCAGGCAACCAGTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAGTCATTACCCGT > minE/464814‑464954
|
| 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
