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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
261,352 |
A→G |
39.7% |
intergenic (‑32/‑119) |
yajI ← / → ybaD |
predicted lipoprotein/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 261,352 | 0 | A | G | 39.7%
| 32.9
/ 53.4
| 78 | intergenic (‑32/‑119) | yajI/ybaD | predicted lipoprotein/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (34/13); new base G (25/6); total (59/19) |
| Fisher's exact test for biased strand distribution p-value = 4.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.66e-01 |
AGCAGGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTATCTCAAAAGCGTTGCGCCTTTGT > minE/261289‑261413
|
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2346784/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:69582/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:55141/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1870749/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1954000/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2017105/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:390657/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2214649/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2276628/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:995214/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1107689/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2480191/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2551878/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:3242153/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:3228147/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:3210616/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2776480/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1592469/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:957045/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1285700/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1340825/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:823686/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:1577700/1‑67 (MQ=255)
agcagGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGT‑‑CAATTAGCCTAGTGGTaga > 1:3373496/1‑69 (MQ=255)
agcagGAGAAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg > 1:2265297/1‑67 (MQ=255)
cGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagc > 1:2366735/1‑69 (MQ=255)
cGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagc > 1:2108132/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:2837569/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:1830116/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:1268854/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:1256621/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:3281408/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:1176869/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagca > 1:1532169/1‑69 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagc > 1:71189/1‑68 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGCAAAagc > 1:3426123/1‑68 (MQ=255)
gAAAAACGTTAGTATTCATAGGTCGTCACTTTCTCGTCGCAATTAGCCTAATGGt > 1:2507312/1‑55 (MQ=255)
aaaCGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg < 1:1620463/51‑1 (MQ=255)
aaaCGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg < 1:409840/51‑1 (MQ=255)
aaaCGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg < 1:2352369/51‑1 (MQ=255)
aaaCGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg < 1:2060429/51‑1 (MQ=255)
aaaCGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAGTgg < 1:1533376/51‑1 (MQ=255)
attATTCTTAGGTCGTCCCTTTCTCGTCGCAATTATCATAGTgg < 1:1522698/42‑1 (MQ=255)
aTTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGa > 1:831328/1‑69 (MQ=255)
aTTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAG‑GGGTAAAAGCAGCGAAAGCATCGAt > 1:1861557/1‑69 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:3299662/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt < 1:341027/36‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:2464925/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:508289/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:1473709/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt < 1:1921388/36‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:2727011/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:232123/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:2265064/1‑36 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca > 1:169160/1‑53 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:1231770/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:510087/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:2822761/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca > 1:2050380/1‑53 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca > 1:2124720/1‑53 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:896927/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:2607685/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca > 1:2645148/1‑53 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:276314/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca > 1:11491/1‑53 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:3067562/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:2992028/53‑1 (MQ=255)
cATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:2952131/53‑1 (MQ=255)
cATAGGACGTCCCTTTCTCGTCGCAATTAGCCTAAt > 1:438828/1‑36 (MQ=255)
aTAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAagca < 1:1397999/52‑1 (MQ=255)
aGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATAGATCCtt < 1:1932476/68‑1 (MQ=255)
gtcgtcCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTAt > 1:1763699/1‑69 (MQ=255)
gtcgtcCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTAt > 1:929271/1‑69 (MQ=255)
ctcGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCTAAAGCATCGATCCTTTATCTCAAAAGCGt > 1:666150/1‑69 (MQ=255)
ctcGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTATCTCAAAAGCGt > 1:632112/1‑69 (MQ=255)
ctcGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTATCTCAAAAGCGt > 1:2280862/1‑69 (MQ=255)
ctcGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTATCTCAAAAGCGt > 1:3207956/1‑69 (MQ=255)
aGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTATCTCAAAAGCGTTGCGCCTttgt > 1:1123577/1‑68 (MQ=255)
|
AGCAGGAGCAGTCGAAAAACGTTAGTATTCATAGGTCGTCCCTTTCTCGTCGCAATTAGCCTAATGGTAGAGGGTAAAAGCAGCGAAAGCATCGATCCTTTATCTCAAAAGCGTTGCGCCTTTGT > minE/261289‑261413
|
| 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
