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 |
775,607 |
C→A |
15.5% |
D410E (GAC→GAA) |
icd → |
isocitrate dehydrogenase, specific for NADP+ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 775,607 | 0 | C | A | 15.5%
| 129.1
/ 8.2
| 45 | D410E (GAC→GAA) | icd | isocitrate dehydrogenase, specific for NADP+ |
| Reads supporting (aligned to +/- strand): ref base C (20/18); new base A (5/2); total (25/20) |
| Fisher's exact test for biased strand distribution p-value = 4.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01 |
AAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGT > minE/775537‑775676
|
aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc < 1:1276596/71‑1 (MQ=255)
aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc < 1:2238057/71‑1 (MQ=255)
ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg < 1:540875/71‑1 (MQ=255)
cGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg > 1:1092867/1‑70 (MQ=255)
aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcat > 1:3354160/1‑71 (MQ=255)
cTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGa < 1:1127717/65‑1 (MQ=255)
tATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCg > 1:1698382/1‑70 (MQ=255)
aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa > 1:2398538/1‑70 (MQ=255)
tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa > 1:2320314/1‑70 (MQ=255)
aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa < 1:950675/70‑1 (MQ=255)
tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATg > 1:932792/1‑71 (MQ=255)
cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagc > 1:1887323/1‑54 (MQ=255)
cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACAt < 1:3071595/69‑1 (MQ=255)
tggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGt < 1:3379597/71‑1 (MQ=255)
ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt > 1:1691546/1‑71 (MQ=255)
tggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa > 1:788489/1‑48 (MQ=255)
gcgcTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa > 1:2936314/1‑56 (MQ=255)
aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt > 1:3725205/1‑70 (MQ=255)
aaaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt > 1:1956097/1‑70 (MQ=255)
aaCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATtta > 1:1062547/1‑71 (MQ=255)
aCTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt < 1:3109982/47‑1 (MQ=255)
aCTGCTGAAATGATCAGAGTTTGGTGACGCGATCATCGaaa > 1:1191619/1‑41 (MQ=255)
ctgctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt < 1:1931516/67‑1 (MQ=255)
ctgctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttat > 1:3094396/1‑70 (MQ=255)
ctgctgAAATGTTCAGAGTTTGGTGAAGCGatcatc > 1:908422/1‑36 (MQ=255)
ctgctgAAATGTTCAGAGTTTGGTGAAGCGatcatc > 1:78610/1‑36 (MQ=255)
gctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTg > 1:3504427/1‑58 (MQ=255)
gctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTg > 1:874273/1‑58 (MQ=255)
ctgAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttatta < 1:3105785/69‑1 (MQ=255)
gAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGcc < 1:3643202/47‑1 (MQ=255)
aaaTGTTCAGAGTTTGGTGACGCGATCATCGaaaa > 1:367322/1‑35 (MQ=255)
aaaTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACggg < 1:1370934/71‑1 (MQ=255)
aaaTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACgg < 1:2763833/70‑1 (MQ=255)
aaaTGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATg < 1:3778791/39‑1 (MQ=255)
aaTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGa < 1:177902/71‑1 (MQ=255)
aTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATg > 1:823773/1‑37 (MQ=255)
aTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGt > 1:194820/1‑38 (MQ=255)
aTGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAg > 1:3261257/1‑71 (MQ=255)
ttCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttatta < 1:3182803/61‑1 (MQ=255)
ttCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATttatta < 1:1991316/61‑1 (MQ=255)
cAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt > 1:1767977/1‑54 (MQ=255)
gagTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAttt > 1:1912298/1‑53 (MQ=255)
agTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt > 1:2393484/1‑51 (MQ=255)
agTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGc > 1:3900617/1‑71 (MQ=255)
tttGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt < 1:1739446/49‑1 (MQ=255)
tttGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAAtt < 1:2623190/49‑1 (MQ=255)
tttGGTGACGCGATAATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGt < 1:712975/64‑1 (MQ=255)
gTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACgg < 1:115158/54‑1 (MQ=255)
tGACGCGATCATCGAAAACATGTAATGCCGTAGTTTg < 1:1420201/37‑1 (MQ=255)
aCGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCgttgt < 1:458473/71‑1 (MQ=255)
cgcgATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTaa > 1:412275/1‑47 (MQ=255)
|
AAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTTTGTTAAATTTATTAACGGGAGCGTAACGCTCCCGTTGT > minE/775537‑775676
|
| 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
