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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,115,786 |
T→C |
30.2% |
intergenic (‑28/+55) |
msyB ← / ← mdtG |
hypothetical protein/predicted drug efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,115,786 | 0 | T | C | 30.2%
| 67.0
/ 44.1
| 53 | intergenic (‑28/+55) | msyB/mdtG | hypothetical protein/predicted drug efflux system |
| Reads supporting (aligned to +/- strand): ref base T (25/12); new base C (10/6); total (35/18) |
| Fisher's exact test for biased strand distribution p-value = 7.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.65e-01 |
CAGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATA > W3110S.gb/1115719‑1115851
|
cAGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGctt < 1:1900177/70‑1 (MQ=255)
tCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAggg > 1:1326192/1‑70 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaa > 1:2180624/1‑70 (MQ=255)
ggCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGttt > 1:1094676/1‑60 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGa < 1:740169/71‑1 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGc > 1:1377426/1‑71 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGa > 1:2102754/1‑67 (MQ=255)
gCGTTGAGTACATGGTCATCACGATTCTCCCTTTGAGTTTATGAGGtt < 1:2332265/48‑1 (MQ=255)
gCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCg < 1:2113867/70‑1 (MQ=255)
gCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCg < 1:2762100/70‑1 (MQ=255)
gTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAg < 1:787388/52‑1 (MQ=255)
tACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaaa < 1:46822/50‑1 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg > 1:1002304/1‑50 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg > 1:5058286/1‑50 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg > 1:2696057/1‑50 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg > 1:4321746/1‑50 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTg > 1:3976345/1‑71 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGaaa > 1:1175978/1‑47 (MQ=255)
gTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaa > 1:2760264/1‑43 (MQ=255)
gTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaa > 1:4707801/1‑43 (MQ=255)
gTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAg > 1:2422353/1‑71 (MQ=255)
atcaCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:1462803/1‑63 (MQ=255)
atcaCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTAt > 1:728359/1‑71 (MQ=255)
tcaCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGa < 1:2028893/37‑1 (MQ=255)
caCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATg > 1:1749968/1‑70 (MQ=255)
caCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATg > 1:4891541/1‑70 (MQ=255)
caCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATg > 1:1709964/1‑70 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaa > 1:1180686/1‑37 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:4639689/70‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCACGGaaa > 1:374205/1‑37 (MQ=255)
cGATTCTCCCTTTGAGTTGATTAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa < 1:1786146/71‑1 (MQ=255)
gATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAg < 1:2958171/71‑1 (MQ=255)
aTTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAgg > 1:1085198/1‑71 (MQ=255)
aTTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAgg > 1:515971/1‑71 (MQ=255)
ttCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGc > 1:1863492/1‑71 (MQ=255)
ttCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGc > 1:361067/1‑71 (MQ=255)
tctcCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGa > 1:2968357/1‑36 (MQ=255)
tctcCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGc > 1:1757394/1‑70 (MQ=255)
ttGAGTTGATGATGTTTCAGGGAAAAGGAATGCTGATTCTCCg < 1:4191813/43‑1 (MQ=37)
ttGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAAt > 1:794401/1‑70 (MQ=255)
tGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAAt > 1:4749096/1‑69 (MQ=255)
tGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAAt > 1:107524/1‑69 (MQ=255)
gAGTTGATGAGGTTTCATGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAg > 1:1658476/1‑71 (MQ=255)
gAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAg > 1:4506949/1‑71 (MQ=255)
gAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAg > 1:156742/1‑71 (MQ=255)
aGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAg < 1:607570/70‑1 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATtct < 1:1258341/35‑1 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTc < 1:3080884/71‑1 (MQ=255)
tgatgaGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:4107447/52‑1 (MQ=255)
tgatgaGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:3373198/52‑1 (MQ=255)
tgatgaGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:211535/52‑1 (MQ=255)
tgatgaGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:1786323/52‑1 (MQ=255)
gatgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGa > 1:1477691/1‑71 (MQ=255)
gatgaGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGa > 1:118354/1‑71 (MQ=255)
tgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:3816537/49‑1 (MQ=255)
tgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATa > 1:2689671/1‑71 (MQ=255)
|
CAGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATA > W3110S.gb/1115719‑1115851
|
| 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
