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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,362,267 |
T→G |
15.2% |
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 | 15.2%
| 79.2
/ 19.6
| 46 | E344A (GAA→GCA) | cadA | lysine decarboxylase 1 |
| Reads supporting (aligned to +/- strand): ref base T (22/17); new base G (4/3); total (26/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.82e-01 |
TTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCC > W3110S.gb/4362198‑4362332
|
ttGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTc > 1:2809419/1‑71 (MQ=255)
tgtgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCg > 1:2520167/1‑71 (MQ=255)
aGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTaa < 1:2749407/70‑1 (MQ=255)
gTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAAt > 1:2534960/1‑71 (MQ=255)
gTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTaaa > 1:2596726/1‑70 (MQ=255)
gTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTaaa > 1:420384/1‑70 (MQ=255)
gTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACATTCGTAAAt > 1:53189/1‑71 (MQ=255)
cTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGt > 1:1755057/1‑70 (MQ=255)
cTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGt > 1:2121319/1‑70 (MQ=255)
tGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTa < 1:1420158/62‑1 (MQ=255)
tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGtt > 1:1192525/1‑71 (MQ=255)
tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGt > 1:407299/1‑70 (MQ=255)
aaTGACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtg > 1:1962322/1‑70 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGGATTTACCTTCGTAAATCGGTGAGAAGTTGgtg > 1:6803/1‑70 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtgt < 1:449981/71‑1 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtg > 1:418847/1‑70 (MQ=255)
aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtg > 1:1034262/1‑70 (MQ=255)
aTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTaa < 1:187330/51‑1 (MQ=255)
cTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAgg > 1:88449/1‑70 (MQ=255)
cTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGc < 1:1918110/71‑1 (MQ=255)
cgacTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCAcc < 1:1855889/68‑1 (MQ=255)
ccTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa > 1:619552/1‑71 (MQ=255)
cTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg > 1:701451/1‑71 (MQ=255)
gCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa < 1:1899201/71‑1 (MQ=255)
ccACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa < 1:251999/70‑1 (MQ=255)
ccGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAgg < 1:2265637/50‑1 (MQ=255)
ccGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg < 1:549100/71‑1 (MQ=255)
ccGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg < 1:1381392/71‑1 (MQ=255)
cGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg < 1:1461076/70‑1 (MQ=255)
gCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga > 1:2617259/1‑71 (MQ=255)
cATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa > 1:979811/1‑63 (MQ=255)
cATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatg > 1:956038/1‑70 (MQ=255)
aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAtt > 1:1400351/1‑71 (MQ=255)
ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg < 1:1556488/62‑1 (MQ=255)
ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt > 1:859354/1‑71 (MQ=255)
ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt > 1:1075424/1‑71 (MQ=255)
ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt > 1:2299731/1‑71 (MQ=255)
cGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg < 1:67543/61‑1 (MQ=255)
cATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca > 1:2047530/1‑70 (MQ=255)
cATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca > 1:1892483/1‑70 (MQ=255)
tttACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa < 1:1498389/53‑1 (MQ=255)
tttACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa < 1:2196869/52‑1 (MQ=255)
tttACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa < 1:1761317/52‑1 (MQ=255)
tttACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa < 1:632261/54‑1 (MQ=255)
aCCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATcc < 1:2489767/70‑1 (MQ=255)
aCCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATcc < 1:2085763/70‑1 (MQ=255)
|
TTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCC > W3110S.gb/4362198‑4362332
|
| 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
