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 |
|
A11 F142 I1 R1
|
99 |
64.8 |
3148104 |
96.3% |
3031624 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,352,993 |
T→A |
I116N (ATC→AAC) |
glpA → |
anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,352,993 | 0 | T | A | 94.1%
| 161.5
/ 2.5
| 51 | I116N (ATC→AAC) | glpA | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base A (25/23); total (26/25) |
| Fisher's exact test for biased strand distribution p-value = 6.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.19e-01 |
TGCGTTGAACCAACCAACGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGATGGCACC > NC_000913/2352899‑2353087
|
tGCGTTGAACCAACCAACGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAgcg < 2:1393257/100‑1 (MQ=255)
gAACCAACCAACGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAg > 1:540713/1‑100 (MQ=255)
ccaaccaaCGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCta > 2:9009/1‑100 (MQ=255)
ccaaccaaCGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCta < 1:789299/100‑1 (MQ=255)
caaccaacGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCCCTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCtat > 2:959997/1‑100 (MQ=255)
caaccaacGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCtat > 1:165986/1‑100 (MQ=255)
aaccaacGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCtata > 2:578233/1‑100 (MQ=255)
acGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGAccc < 2:1168233/100‑1 (MQ=255)
acGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGAccc < 2:1167142/100‑1 (MQ=255)
cTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCgcagc < 2:991864/100‑1 (MQ=255)
ttATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAgc < 1:123955/100‑1 (MQ=255)
tCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAgcgcg < 1:1327155/100‑1 (MQ=255)
aCCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCa > 1:849504/1‑100 (MQ=255)
cccTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCAt > 2:1298828/1‑100 (MQ=255)
cccTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCAt > 1:190402/1‑100 (MQ=255)
ccTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCAtt > 1:1053882/1‑100 (MQ=255)
gCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATc > 1:754593/1‑100 (MQ=255)
ccGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCg > 1:1297811/1‑100 (MQ=255)
cgcaaGACGCCCTGTCCTGCCAGGCCACATTGAGTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATc < 2:1370540/95‑1 (MQ=255)
ggAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGTGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGaa < 2:1100538/100‑1 (MQ=255)
ggAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGaa > 1:1004092/1‑100 (MQ=255)
ggAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGaa > 1:1215108/1‑100 (MQ=255)
ggAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGaa > 1:692349/1‑100 (MQ=255)
gAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAAc < 1:1364739/100‑1 (MQ=255)
aTGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGc < 2:540710/100‑1 (MQ=255)
gACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGc > 2:1352465/1‑98 (MQ=255)
gACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCg > 2:377531/1‑100 (MQ=255)
gACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCg < 1:1562573/100‑1 (MQ=255)
ccTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGtt < 1:1155692/100‑1 (MQ=255)
ccTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGtt > 1:175619/1‑100 (MQ=255)
tctcCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTaa > 2:796883/1‑100 (MQ=255)
ctcCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAAc > 1:1178863/1‑100 (MQ=255)
ccTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGA‑CCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCg < 2:1149609/100‑1 (MQ=255)
cTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCg > 1:151507/1‑100 (MQ=255)
cTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCg > 2:1305807/1‑100 (MQ=255)
cTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCg < 1:1372705/100‑1 (MQ=255)
cAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCAc < 2:1053875/100‑1 (MQ=255)
cTTTTATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATCATCGAACCTGCCGTTAACCCGGCACTGATTgg > 2:1162027/1‑100 (MQ=255)
ttttATTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGgc > 1:910110/1‑100 (MQ=255)
aTTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCgg < 1:1298837/100‑1 (MQ=255)
aTTCGCGCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCgg < 1:737054/100‑1 (MQ=255)
cgcgCCTGCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGa > 2:1048927/1‑100 (MQ=255)
gCGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTcc < 2:407905/100‑1 (MQ=255)
cGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCg < 2:920361/100‑1 (MQ=255)
cGAAGAAGCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCg < 2:921120/100‑1 (MQ=255)
gatctagCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCgg < 2:173948/95‑1 (MQ=255)
gaagCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGATg > 2:562265/1‑100 (MQ=255)
gaagCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGATg < 2:692346/100‑1 (MQ=255)
aagCAGGGAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGATgg < 1:1129214/100‑1 (MQ=255)
agCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGagatc > 1:173948/1‑96 (MQ=255)
ggAACAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGATGGCAcc < 1:208947/98‑1 (MQ=255)
|
TGCGTTGAACCAACCAACGGCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGAACCTGCCGTTAACCCGGCACTGATTGGCGCGGTGAAAGTTCCGGATGGCACC > NC_000913/2352899‑2353087
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
