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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,503,968 |
G→A |
50.0% |
A297A (GCG→GCA) |
uhpT → |
hexose phosphate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,503,968 | 0 | G | A | 50.0%
| ‑5.2
/ 39.8
| 46 | A297A (GCG→GCA) | uhpT | hexose phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base G (15/8); new base A (8/15); total (23/23) |
| Fisher's exact test for biased strand distribution p-value = 7.58e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01 |
TATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGGGCTGG > minE/2503902‑2504028
|
tATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGa > 1:3307075/1‑68 (MQ=255)
tATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGa > 1:743231/1‑68 (MQ=255)
gTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGt > 1:1586840/1‑68 (MQ=255)
tataCGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTg > 1:1844258/1‑69 (MQ=255)
tataCGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTg > 1:1772548/1‑69 (MQ=255)
tataCGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTg > 1:1440955/1‑69 (MQ=255)
tataCGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTg > 1:3006703/1‑69 (MQ=255)
cgTTCCATGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTgcct < 1:676161/69‑3 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:2880828/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:2082610/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:1981454/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:2114959/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:1313435/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:2748845/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:2984967/1‑57 (MQ=255)
cgTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTg > 1:2831344/1‑57 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:321012/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:2132022/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:3006365/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1677914/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:449862/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:486870/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1548833/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1523492/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1504946/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1298032/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:858789/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1247485/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:1184025/68‑1 (MQ=255)
ttCCAGGAACTGAAACTCTCTAAAGCGGTGGCAATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCt < 1:999546/68‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCTGTGGCGATTCAGGGCTTTAGGCTGTTTTAAGCTTGTGCGCTGGTCgg < 1:212842/69‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTTGTGCGCTGGTCgg < 1:164238/69‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCgg < 1:2605802/69‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCgg < 1:1078012/69‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCgg < 1:206481/69‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCgg < 1:1478837/69‑1 (MQ=255)
ggAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCgg < 1:763173/69‑1 (MQ=255)
gAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAGGCTGGTGCGCTGGTCGGTACgct > 1:2116453/1‑69 (MQ=255)
tAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTgggg > 1:1144378/1‑69 (MQ=255)
aaGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggct > 1:2755911/1‑69 (MQ=255)
aaGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggct > 1:1282726/1‑69 (MQ=255)
aaGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggct > 1:951137/1‑69 (MQ=255)
aGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggctg > 1:2773806/1‑69 (MQ=255)
aGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggctg > 1:340935/1‑69 (MQ=255)
aGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggctg > 1:916339/1‑69 (MQ=255)
gCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGggctgg < 1:1638773/69‑1 (MQ=255)
|
TATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGGGCTGG > minE/2503902‑2504028
|
| 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
