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 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,362,267 |
T→G |
42.7% |
E344A (GAA→GCA) |
cadA ← |
lysine decarboxylase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,362,267 | 0 | T | G | 42.7%
| 0.2
/ 102.2
| 68 | E344A (GAA→GCA) | cadA | lysine decarboxylase 1 |
| Reads supporting (aligned to +/- strand): ref base T (25/14); new base G (14/15); total (39/29) |
| Fisher's exact test for biased strand distribution p-value = 2.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGT > W3110S.gb/4362201‑4362335
|
tgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTa < 1:1190824/71‑1 (MQ=255)
tgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTa < 1:425064/71‑1 (MQ=255)
tGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATc < 1:708723/71‑1 (MQ=255)
gACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCg < 1:717063/70‑1 (MQ=255)
ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgag > 1:2441853/1‑70 (MQ=255)
ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgag > 1:2182978/1‑70 (MQ=255)
ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCg > 1:3768217/1‑65 (MQ=255)
ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTgag > 1:3728915/1‑70 (MQ=255)
ggTTTCGTAAATCACTTTCCCTTCTACAAGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgag > 1:443657/1‑70 (MQ=255)
tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt > 1:922283/1‑71 (MQ=255)
tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt > 1:2651945/1‑71 (MQ=255)
tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt > 1:3340154/1‑71 (MQ=255)
tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGt < 1:3084460/70‑1 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtgt < 1:38454/71‑1 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATc > 1:685918/1‑55 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATc > 1:2506383/1‑55 (MQ=255)
aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa < 1:1512271/71‑1 (MQ=255)
aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa < 1:2922305/71‑1 (MQ=255)
aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa < 1:706283/71‑1 (MQ=255)
aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa < 1:574036/71‑1 (MQ=255)
aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa < 1:1291971/71‑1 (MQ=255)
tCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt < 1:1131424/64‑1 (MQ=255)
aCTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAgg < 1:2338781/71‑1 (MQ=255)
cTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGc < 1:3653497/71‑1 (MQ=255)
ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa > 1:1331661/1‑71 (MQ=255)
ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa > 1:3239856/1‑71 (MQ=255)
ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa > 1:2922572/1‑71 (MQ=255)
ccTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa < 1:3311922/71‑1 (MQ=255)
ccTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa < 1:318095/71‑1 (MQ=255)
cacGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg < 1:3228256/68‑1 (MQ=255)
cacGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAg > 1:2323106/1‑71 (MQ=255)
ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa < 1:132007/71‑1 (MQ=255)
ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa < 1:3495092/71‑1 (MQ=255)
ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa < 1:3228847/71‑1 (MQ=255)
ggCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa < 1:196573/71‑1 (MQ=255)
gCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa < 1:3011612/71‑1 (MQ=255)
gCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa < 1:3812125/71‑1 (MQ=255)
cACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTa < 1:2546045/49‑1 (MQ=255)
aCCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGt > 1:4078803/1‑71 (MQ=255)
gCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga > 1:1265889/1‑71 (MQ=255)
gCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga > 1:2502468/1‑71 (MQ=255)
cTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAgg < 1:2952766/47‑1 (MQ=255)
cTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAgg < 1:3584495/47‑1 (MQ=255)
cATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCa > 1:341657/1‑47 (MQ=255)
aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTaa > 1:3073677/1‑40 (MQ=255)
aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa > 1:3157642/1‑60 (MQ=255)
aCCGCATTTACATTCGTAAATCGGTGAGAAGTTGGTGTaa > 1:1100546/1‑40 (MQ=255)
ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAtt > 1:1968202/1‑70 (MQ=255)
ccGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTaa > 1:2107495/1‑39 (MQ=255)
cGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatgg < 1:112867/66‑1 (MQ=255)
cGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatgg < 1:2037364/66‑1 (MQ=255)
gCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca > 1:1757102/1‑71 (MQ=255)
gCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca > 1:2592196/1‑71 (MQ=255)
gCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTggatggat > 1:2045108/1‑67 (MQ=255)
cATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTggatggat > 1:2465077/1‑66 (MQ=255)
cATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTggatggat > 1:3903628/1‑66 (MQ=255)
cATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca > 1:44845/1‑70 (MQ=255)
tttACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACAt > 1:2289126/1‑71 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa > 1:484831/1‑40 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa > 1:2799045/1‑52 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa > 1:2848326/1‑52 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa > 1:3219242/1‑52 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa > 1:1144805/1‑50 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAg > 1:427565/1‑53 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAg > 1:143063/1‑53 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc > 1:4017136/1‑70 (MQ=255)
tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc > 1:1829940/1‑70 (MQ=255)
cTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAgt < 1:36481/71‑1 (MQ=255)
|
TGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGT > W3110S.gb/4362201‑4362335
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
