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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,692,839 |
G→A |
67.9% |
G425D (GGT→GAT) |
ydgA → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,692,839 | 0 | G | A | 67.9%
| 62.8
/ 46.9
| 53 | G425D (GGT→GAT) | ydgA | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (8/9); new base A (23/13); total (31/22) |
| Fisher's exact test for biased strand distribution p-value = 3.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
GACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCA > W3110S.gb/1692783‑1692905
|
gACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGAt > 1:2121348/1‑70 (MQ=255)
gACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGAt > 1:1581095/1‑70 (MQ=255)
aCCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCa < 1:1693948/71‑1 (MQ=255)
ttCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCg < 1:1649815/71‑1 (MQ=255)
tCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCg > 1:2429299/1‑70 (MQ=255)
tCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCg > 1:395213/1‑70 (MQ=255)
tCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCg > 1:198413/1‑70 (MQ=255)
tCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCg > 1:2909866/1‑70 (MQ=255)
tCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCg > 1:151228/1‑70 (MQ=255)
tGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGaaaaaa > 1:2585166/1‑71 (MQ=255)
gATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:2530968/1‑71 (MQ=255)
gATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:251217/1‑71 (MQ=255)
gCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTAt > 1:3612037/1‑42 (MQ=255)
gCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTAt > 1:596484/1‑42 (MQ=255)
gCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTAt > 1:2543725/1‑42 (MQ=255)
gCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTAt > 1:94159/1‑42 (MQ=255)
aCTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGa < 1:3178434/47‑1 (MQ=255)
aCTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGa < 1:3246399/47‑1 (MQ=255)
aCTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGa < 1:947243/47‑1 (MQ=255)
aTGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTg < 1:312786/70‑1 (MQ=255)
aCTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa < 1:2657434/55‑1 (MQ=255)
gTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg < 1:2353675/67‑1 (MQ=255)
gTAGCGAAGCTGGAAGGTTATCAGGAAGATC‑AGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg < 1:3233855/66‑1 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCa > 1:3695919/1‑68 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCAt > 1:387296/1‑69 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCAt > 1:3079708/1‑69 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCAt > 1:1551785/1‑69 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCAt > 1:2211095/1‑69 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCa > 1:1565284/1‑67 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCa > 1:448289/1‑67 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCa > 1:1867227/1‑67 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCa > 1:676910/1‑67 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCa > 1:1273133/1‑67 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:3693156/1‑71 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:3689125/1‑71 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:3292297/1‑71 (MQ=255)
aGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:104030/1‑71 (MQ=255)
aGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:3160562/1‑71 (MQ=255)
aGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:2494339/1‑71 (MQ=255)
aGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAg > 1:218677/1‑71 (MQ=255)
gCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg < 1:1838447/64‑1 (MQ=255)
gCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg < 1:731210/64‑1 (MQ=255)
gCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg < 1:903296/64‑1 (MQ=255)
gCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg < 1:961587/64‑1 (MQ=255)
gCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGc < 1:315772/71‑1 (MQ=255)
gCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGc < 1:1864433/71‑1 (MQ=255)
cGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCa < 1:3200283/71‑1 (MQ=255)
cGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCa < 1:840553/71‑1 (MQ=255)
cGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCa < 1:1030755/71‑1 (MQ=255)
gAAGGTTATCAGGAAGATCAAGCTAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCa < 1:127434/71‑1 (MQ=255)
gAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCa < 1:154255/71‑1 (MQ=255)
aaGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCa < 1:3088100/70‑1 (MQ=255)
aaGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa < 1:2530422/36‑1 (MQ=255)
|
GACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCAATGGGGCA > W3110S.gb/1692783‑1692905
|
| 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
