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 |
|
A73 F1 I1 R1
|
21 |
62.0 |
3993596 |
96.1% |
3837845 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,686,827 |
C→T |
A292V (GCC→GTC) |
gabD → |
succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,686,827 | 0 | C | T | 96.5%
| 100.8
/ ‑3.7
| 29 | A292V (GCC→GTC) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (11/17); total (12/17) |
| Fisher's exact test for biased strand distribution p-value = 4.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.54e-01 |
GCCGACCTCGACAAAGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGCCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGCGGTGA > REL606/2686754‑2686892
|
gCCGACCTCGACAAAGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCa > 1:491756/1‑76 (MQ=255)
ccGACCTCGACAAAGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCaa < 1:698977/76‑1 (MQ=255)
gACAAAGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTtat < 2:1233902/76‑1 (MQ=255)
aGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTg < 2:1862672/76‑1 (MQ=255)
aGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTg < 2:1064052/76‑1 (MQ=255)
aGCCGGGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTg < 2:660785/76‑1 (MQ=255)
gTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGCCAACCGTTTATACGTGCAgg > 1:345310/1‑76 (MQ=255)
ggAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGAc > 1:303093/1‑76 (MQ=255)
gAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACg < 2:1770585/76‑1 (MQ=255)
aGGGGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGc < 2:998335/76‑1 (MQ=255)
tGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCgtg < 2:597657/76‑1 (MQ=255)
cTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATg > 1:1203943/1‑76 (MQ=255)
tGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGa < 1:466550/76‑1 (MQ=255)
tGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGa > 2:991569/1‑76 (MQ=255)
gTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGAc > 1:1266220/1‑76 (MQ=255)
tCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGAcc < 1:928332/76‑1 (MQ=255)
ccTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCg > 1:1848142/1‑76 (MQ=255)
cGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCtt > 2:1279422/1‑76 (MQ=255)
cGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCtt < 2:3009/76‑1 (MQ=255)
aaaTTCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTg < 1:1395803/76‑1 (MQ=255)
ttCCGCAACGCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCg > 2:1069998/1‑76 (MQ=255)
gCCGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTgc < 2:638456/76‑1 (MQ=255)
cGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTgcag < 2:1564572/76‑1 (MQ=255)
cGGGCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTgcag > 1:1275161/1‑76 (MQ=255)
ggCAAACCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTgcagca < 1:193036/76‑1 (MQ=255)
aaaCCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGc > 2:903634/1‑76 (MQ=255)
aaaCCTGCGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGc < 1:1026435/76‑1 (MQ=255)
aaaCCTGCGTCTGCGTCAACCGTTTATACGTACAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGc < 2:845293/76‑1 (MQ=255)
aaaCCTGAGTCTGCGTCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGc > 2:861240/1‑76 (MQ=255)
ctgcgtctgcgtCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGCGGTg < 2:521197/76‑1 (MQ=255)
tgcgtctgcgtcAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGCGGTGa < 2:352504/76‑1 (MQ=255)
|
GCCGACCTCGACAAAGCCGTGGAAGGTGCGCTGTCCTCGAAATTCCGCAACGCCGGGCAAACCTGCGTCTGCGCCAACCGTTTATACGTGCAGGACGGCGTGTATGACCGCTTTGCCGAAAAATTGCAGCAGGCGGTGA > REL606/2686754‑2686892
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
