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 |
1,075,721 |
T→C |
49.3% |
S300S (AGT→AGC) |
ydhS → |
conserved hypothetical protein with FAD/NAD(P)‑binding domain |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,075,721 | 0 | T | C | 49.3%
| ‑6.2
/ 67.8
| 73 | S300S (AGT→AGC) | ydhS | conserved hypothetical protein with FAD/NAD(P)‑binding domain |
| Reads supporting (aligned to +/- strand): ref base T (22/15); new base C (17/19); total (39/34) |
| Fisher's exact test for biased strand distribution p-value = 3.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.29e-01 |
CTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTGGTTTGCCGAG > minE/1075659‑1075781
|
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:2318365/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:372242/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:358034/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:3359661/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:3077338/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:2884842/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:2872448/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:2868474/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:261833/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:2444110/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:677179/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:207371/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:1654661/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:1560485/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:889786/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:1152038/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:755702/69‑1 (MQ=255)
cTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:832800/69‑1 (MQ=255)
ttGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCa > 1:2489231/1‑67 (MQ=255)
ttGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATa > 1:2488466/1‑69 (MQ=255)
ttGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATa > 1:3158021/1‑69 (MQ=255)
ttGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATa > 1:1795161/1‑69 (MQ=255)
gATCGGGTATTTAGATTGATAGTAGAGGAAATCAAATTTGCTGATCCAGACTGGAGCCAACGc < 1:2920050/63‑1 (MQ=255)
cGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa < 1:1796322/69‑1 (MQ=255)
cGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa < 1:475954/69‑1 (MQ=255)
cGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa < 1:2744411/69‑1 (MQ=255)
cGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa < 1:1653310/69‑1 (MQ=255)
tAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTTGAGTCAACGCATAGCCTTAGAGAGcc > 1:821981/1‑68 (MQ=255)
tAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGcc > 1:2008998/1‑68 (MQ=255)
tAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGcc > 1:3124981/1‑68 (MQ=255)
tAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGcc > 1:701086/1‑68 (MQ=255)
tAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGcc > 1:2471498/1‑68 (MQ=255)
gATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTg < 1:103532/68‑1 (MQ=255)
aTTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTg < 1:168631/67‑1 (MQ=255)
gtagAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGAt < 1:689700/69‑1 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:55385/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:1508524/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:2067633/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:3227903/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:2174309/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:311877/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:2286978/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:2919332/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:236016/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:1242093/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:1163065/1‑39 (MQ=255)
aaGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTa > 1:103014/1‑39 (MQ=255)
gTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGc < 1:173608/69‑1 (MQ=255)
tGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:605434/69‑1 (MQ=255)
tGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:1121763/69‑1 (MQ=255)
tGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:3121055/69‑1 (MQ=255)
tGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:645418/69‑1 (MQ=255)
tGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:2105299/69‑1 (MQ=255)
tGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:1449545/69‑1 (MQ=255)
gCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTg < 1:3070106/68‑1 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGt > 1:652914/1‑41 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:580724/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:2595918/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:748159/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:3194488/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:3057404/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:2884305/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:2875074/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:2840123/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:2470109/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:2234016/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:144971/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:1258787/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:1073004/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:1071640/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:1043083/1‑42 (MQ=255)
ccAGACTGGAGCCAACGCATAGCCTTAGAAAGCCTGAATGTc > 1:1033365/1‑42 (MQ=255)
gACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTGGTTTGCCGAg > 1:1469632/1‑69 (MQ=255)
|
CTTTTGGATCGGGTATTTAGATTGATAGTAGAGGAAATCAAGTTTGCTGATCCAGACTGGAGTCAACGCATAGCCTTAGAGAGCCTGAATGTCGATTCCTTTGCTCAAGCCTGGTTTGCCGAG > minE/1075659‑1075781
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
