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 |
2,512,687 |
Δ1 bp |
100% |
coding (654/1248 nt) |
ypdG ← |
predicted enzyme IIC component of PTS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,512,687 | 0 | G | . | 96.7%
| 111.0
/ ‑1.6
| 30 | coding (654/1248 nt) | ypdG | predicted enzyme IIC component of PTS |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base . (16/13); total (17/13) |
| 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 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CAGCGCGCCCTTCTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGAATCGGGAGCAAAAATGTGG > W3110S.gb/2512621‑2512754
|
cAGCGCGCCCTTCTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCTAGCCACCAAAggggt > 1:2279141/1‑70 (MQ=255)
cAGCGCGCCCTTCTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt > 1:3438440/1‑70 (MQ=255)
cTTCTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACg > 1:2483004/1‑69 (MQ=255)
ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg > 1:3683605/1‑56 (MQ=255)
ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg > 1:2247557/1‑56 (MQ=255)
ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtagta > 1:1836771/1‑71 (MQ=255)
ctcACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACgtag < 1:1564492/69‑1 (MQ=255)
gCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGc < 1:2606124/71‑1 (MQ=255)
gCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGc < 1:239542/71‑1 (MQ=255)
gTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt < 1:897357/46‑2 (MQ=255)
gTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt < 1:2731816/46‑2 (MQ=255)
gTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt < 1:2332786/46‑2 (MQ=255)
gTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt < 1:2247512/46‑2 (MQ=255)
gTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt < 1:1837145/46‑2 (MQ=255)
tCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAggggt < 1:1687749/45‑2 (MQ=255)
tCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg < 1:697284/42‑1 (MQ=255)
tCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg < 1:2007574/42‑1 (MQ=255)
tCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg < 1:1434119/42‑1 (MQ=255)
tCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg < 1:2463058/42‑1 (MQ=255)
cAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg < 1:2655955/41‑1 (MQ=255)
cAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAgg < 1:2467377/41‑1 (MQ=255)
cAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGa > 1:1731060/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGc > 1:1063488/1‑61 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGc > 1:2972631/1‑61 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGc > 1:1203000/1‑61 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGc > 1:2685224/1‑61 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:2362592/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:1548488/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:1336112/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc < 1:1678726/70‑1 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc < 1:2246983/70‑1 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:2174688/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:1147000/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:3032005/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:3008667/1‑70 (MQ=255)
aGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGAc > 1:1879440/1‑70 (MQ=255)
cGGATACCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCg < 1:1857116/71‑1 (MQ=255)
aCCGCCGTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGa > 1:1780703/1‑68 (MQ=255)
ccgccgTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGa < 1:3441242/71‑1 (MQ=255)
ccgTTGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGc < 1:2876958/47‑1 (MQ=255)
ttGATCCAGCCACCAAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACaaa < 1:2961677/52‑1 (MQ=255)
ccaAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGa < 1:2892870/53‑1 (MQ=255)
ccaAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGa < 1:113517/53‑1 (MQ=255)
ccaAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGa < 1:375158/53‑1 (MQ=255)
ccaAA‑GGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGAATCGGGAGCaaa < 1:13248/65‑1 (MQ=255)
aaaGGGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGAATCGGGAGCAAAAATGTgg > 1:1248241/1‑71 (MQ=255)
|
CAGCGCGCCCTTCTCACCTGCGGCAGTCAGCACAGTACGGATACCGCCGTTGATCCAGCCACCAAAGGGGGTGATGACGTAGTACATCGCCAGCATGACAAAAATGGCGGAAAGAATCGGGAGCAAAAATGTGG > W3110S.gb/2512621‑2512754
|
| 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
