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 |
|
A5 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,055,413 |
A→G |
20.0% |
D396D (GAT→GAC) |
torS ← |
hybrid sensory histidine kinase in two‑component regulatory system with TorR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,055,413 | 0 | A | G | 20.0%
| 81.5
/ 17.6
| 40 | D396D (GAT→GAC) | torS | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| Reads supporting (aligned to +/- strand): ref base A (19/13); new base G (5/3); total (24/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01 |
GCGCTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGAAAGGGGAGTCAATATCAC > W3110S.gb/1055346‑1055483
|
gcgcTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGcatcc < 1:3247457/71‑1 (MQ=255)
gcTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGcgtccat < 1:721450/71‑1 (MQ=255)
gcTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGcatccat > 1:4097863/1‑71 (MQ=255)
gcTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGcatccat < 1:705798/71‑1 (MQ=255)
cTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGcgtccat < 1:237966/70‑1 (MQ=255)
ttGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAg > 1:2023649/1‑71 (MQ=255)
tGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAgc > 1:113310/1‑71 (MQ=255)
tGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAgc > 1:469797/1‑71 (MQ=255)
tGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAg < 1:4349011/70‑1 (MQ=255)
aCCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAgccg < 1:3358502/71‑1 (MQ=255)
aCCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAg < 1:2524050/68‑1 (MQ=255)
gcgcCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAgccg > 1:3590468/1‑67 (MQ=255)
cgccgcCAGCTGTTCGCGGTGGCGATTCAGTGGATGAACATTGCTGCGAAACGCGTCCATCAGCCGCCCGa > 1:1165469/1‑71 (MQ=255)
gccgccAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGAt > 1:1373977/1‑71 (MQ=255)
aGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCGTCCATCAGCCGCCCGATGGTATc > 1:4605718/1‑71 (MQ=255)
gCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATcc < 1:1522862/71‑1 (MQ=255)
cTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATc > 1:2613948/1‑69 (MQ=255)
tGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCGTCCATCAGCCGCCCGATGGt < 1:3496559/65‑1 (MQ=255)
ttCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCGTCCATCAGCCGCCCGa < 1:1555598/59‑1 (MQ=255)
cgcgGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTcc > 1:2085831/1‑71 (MQ=255)
ggTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTAt > 1:3004885/1‑60 (MQ=255)
ggTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCg > 1:3644034/1‑70 (MQ=255)
gTGGCGATTCAGTGCATGAACATTGCTGCGAAACGcgtccat < 1:4138349/42‑1 (MQ=255)
gCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGc < 1:2123708/71‑1 (MQ=255)
gCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGc < 1:1057911/71‑1 (MQ=255)
gCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGc > 1:1205315/1‑71 (MQ=255)
gATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGAt > 1:287745/1‑49 (MQ=255)
gATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTa < 1:1226026/66‑1 (MQ=255)
aTTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTACCGTACGCCAg > 1:3007469/1‑71 (MQ=255)
ttCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGc > 1:264010/1‑71 (MQ=255)
ttCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGc > 1:1994142/1‑71 (MQ=255)
tCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTcc < 1:1952714/59‑1 (MQ=255)
tCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCg > 1:2899791/1‑71 (MQ=255)
tCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCg > 1:3926201/1‑71 (MQ=255)
cAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGt > 1:4197041/1‑61 (MQ=255)
aGTGCATGAACATTGCTGCGAAACGCGTCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGt > 1:2600341/1‑71 (MQ=255)
tGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGa < 1:4097017/41‑1 (MQ=255)
cATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGc < 1:801864/50‑1 (MQ=255)
cATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTcc < 1:1530058/71‑1 (MQ=255)
tGAACATTGCTGCGAAACGCGTCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCgg > 1:788617/1‑71 (MQ=255)
gAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCgg > 1:157215/1‑70 (MQ=255)
aaCATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGa < 1:1387466/71‑1 (MQ=255)
cATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACg < 1:1656428/53‑1 (MQ=255)
tgctgcGAAACGCGTCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGAAAggg > 1:367313/1‑71 (MQ=255)
gctgcGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGAAAggg > 1:3723464/1‑70 (MQ=255)
gAAACGCGTCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGaaa < 1:3045276/62‑1 (MQ=255)
catccatcAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGAAAGGGGAGTCaa > 1:119952/1‑66 (MQ=255)
atccatcAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGAAAGGGGAGTCAATATCAc > 1:4500544/1‑71 (MQ=255)
|
GCGCTTTGACCTGCGCCGCCAGCTGTTCGCGGTGGCGATTCAGTGCATGAACATTGCTGCGAAACGCATCCATCAGCCGCCCGATGGTATCCAGCTCCCGTACGCCAGCGGTTTCCGGGAAAGGGGAGTCAATATCAC > W3110S.gb/1055346‑1055483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
