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 R1
|
148 |
22.8 |
1772010 |
97.0% |
1718849 |
61.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,115,786 |
T→C |
57.1% |
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 | 57.1%
| 6.4
/ 22.6
| 21 | intergenic (‑28/+55) | msyB/mdtG | hypothetical protein/predicted drug efflux system |
| Reads supporting (aligned to +/- strand): ref base T (4/5); new base C (5/7); total (9/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTC > W3110S.gb/1115720‑1115847
|
aGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGttt > 1:1092380/1‑69 (MQ=255)
tGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAg > 1:1243035/1‑71 (MQ=255)
ggCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAg > 1:1421773/1‑70 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGa > 1:1093343/1‑71 (MQ=255)
tcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCt > 1:285883/1‑70 (MQ=255)
aaGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGa < 1:1301010/70‑1 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATtct > 1:32593/1‑62 (MQ=255)
cATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCg > 1:1388016/1‑65 (MQ=255)
atcaCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTAt < 1:516684/71‑1 (MQ=255)
atcaCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTa < 1:1466179/70‑1 (MQ=255)
tcaCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCt < 1:1544923/59‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaa < 1:339573/71‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGc > 1:1309299/1‑56 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCaa < 1:225658/64‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaa < 1:564730/71‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa > 1:409438/1‑70 (MQ=255)
gATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAg > 1:928868/1‑71 (MQ=255)
aTTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa < 1:584594/45‑1 (MQ=255)
cTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAg < 1:1576906/55‑1 (MQ=255)
cTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaaa < 1:1026488/71‑1 (MQ=255)
gTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGt < 1:1741316/70‑1 (MQ=255)
ttGATGAGGCTTCAGGGAAAAGGATAGATGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTc < 1:669363/71‑1 (MQ=255)
|
AGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTC > W3110S.gb/1115720‑1115847
|
| 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
