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 |
|
A11 F1 I1 R1
|
757 |
76.1 |
3598070 |
93.4% |
3360597 |
108.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,160,196 |
T→C |
V604A (GTG→GCG) |
mdtC → |
multidrug efflux system, subunit C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,160,196 | 0 | T | C | 98.2%
| 195.5
/ ‑3.8
| 56 | V604A (GTG→GCG) | mdtC | multidrug efflux system, subunit C |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (28/27); minor base G (1/0); total (29/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 |
TTGATGGGCGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGTGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATGGCGGTA > NC_000913/2160063‑2160326
|
ttGATGGGCGGGATTAAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACa > 1:1202378/1‑139 (MQ=255)
gggCGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCggg < 1:1766877/139‑1 (MQ=255)
cGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGgatg < 2:480841/139‑1 (MQ=255)
cGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGgatg < 1:853545/139‑1 (MQ=255)
aGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTAt < 1:196759/139‑1 (MQ=255)
aTCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCt > 2:1249357/1‑139 (MQ=255)
ttCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATACTGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGgatg > 1:497052/1‑115 (MQ=255)
ttCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGgatg < 2:497052/115‑1 (MQ=255)
cGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGcga > 2:8699/1‑139 (MQ=255)
ttCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGcgacga > 1:881344/1‑139 (MQ=255)
cAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGaa < 1:677841/98‑1 (MQ=255)
cAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGaa > 2:677841/1‑98 (MQ=255)
cAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGgatg < 2:304312/108‑1 (MQ=255)
cAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGgatg > 1:304312/1‑108 (MQ=255)
tGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTAt < 2:1531894/109‑1 (MQ=255)
tGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTAt > 1:1531894/1‑109 (MQ=255)
gcgGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAAc < 2:881344/139‑1 (MQ=255)
tGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGGGAACAGCGGGATGATGTTTATCACCCTAAAGCCACGCGACGAACGCAGCGAAACGGCgcagca > 2:1082972/1‑139 (MQ=255)
gATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGGGGTTCGCGAGCGAACAGCGGGATGATGTTTAt > 1:1186014/1‑92 (MQ=255)
gATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCggg < 2:906584/81‑1 (MQ=255)
gATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCggg > 1:906584/1‑81 (MQ=255)
gATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTAt < 2:1186014/92‑1 (MQ=255)
tttCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCAc > 2:1503422/1‑104 (MQ=255)
tttCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCAc < 1:1503422/104‑1 (MQ=255)
tttCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATc > 2:620139/1‑139 (MQ=255)
tCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGa > 2:175332/1‑139 (MQ=255)
tCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCA‑CCTCAAGCCACGCGACGAACGCAGCGAAACGgcg < 1:1625419/124‑1 (MQ=255)
tCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCA‑CCTCAAGCCACGCGACGAACGCAGCGAAACGgcg > 2:1625419/1‑124 (MQ=255)
tGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCg > 2:66789/1‑139 (MQ=255)
tCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGa < 2:607895/127‑1 (MQ=255)
tCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGa > 1:607895/1‑127 (MQ=255)
ccGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTa < 1:620139/139‑1 (MQ=255)
gACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTAt < 1:1324691/71‑1 (MQ=255)
gACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTAt > 2:1324691/1‑71 (MQ=255)
tCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACgg > 2:676350/1‑101 (MQ=255)
tCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACgg < 1:676350/101‑1 (MQ=255)
tGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAAcc > 1:581088/1‑139 (MQ=255)
gATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGga > 2:931945/1‑46 (MQ=255)
gATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGga < 1:931945/46‑1 (MQ=255)
gATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAAc < 2:1261076/136‑1 (MQ=255)
gATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAAc > 1:1261076/1‑136 (MQ=255)
gATAATGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCgg > 2:973937/1‑139 (MQ=255)
tGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGaaa > 2:62797/1‑83 (MQ=255)
tGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGaaa < 1:62797/83‑1 (MQ=255)
tGTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCg > 1:880118/1‑139 (MQ=255)
gTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGa < 1:93370/139‑1 (MQ=255)
gTCACCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGa < 2:880118/139‑1 (MQ=255)
aCCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGaaa > 2:601071/1‑79 (MQ=255)
aCCGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGaaa < 1:601071/79‑1 (MQ=255)
ccGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACgg < 2:1173996/81‑1 (MQ=255)
ccGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCt > 2:82473/1‑139 (MQ=255)
ccGGCTTTACAGGCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCCACGAACGCAGCGAAACgg > 1:1173996/1‑81 (MQ=255)
ggCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATgg < 1:1249357/139‑1 (MQ=255)
ggCGGTTCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATgg < 2:1617867/139‑1 (MQ=255)
ttCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATGGCGGTa > 1:1411195/1‑139 (MQ=255)
ttCGCGAGCGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATGGCGGTa < 1:175332/139‑1 (MQ=255)
|
TTGATGGGCGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGTGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATGGCGGTA > NC_000913/2160063‑2160326
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
