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 |
3,232,470 |
A→G |
79.0% |
L111L (TTG→CTG) |
ygjM ← |
predicted DNA‑binding transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,232,470 | 0 | A | G | 79.0%
| 79.0
/ 16.5
| 38 | L111L (TTG→CTG) | ygjM | predicted DNA‑binding transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base A (6/2); new base G (19/11); total (25/13) |
| Fisher's exact test for biased strand distribution p-value = 6.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01 |
GGGAGAAATGCCGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAAAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAACCATATTGATC > W3110S.gb/3232402‑3232536
|
gggAGAAATGCCGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCaaa < 1:583397/70‑1 (MQ=255)
agaAATGCCGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAAcgc > 1:1557082/1‑71 (MQ=255)
aTGCCGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCagaa > 1:1692065/1‑64 (MQ=255)
tGCCGAATCGCGTTGCCAA‑TTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGt < 1:196325/67‑1 (MQ=255)
gCCGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGaca > 1:2411742/1‑71 (MQ=255)
gCCGAATCGCGTTGCCAAATTTTTAGGGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAAAACGCGTGaca > 1:461835/1‑71 (MQ=255)
ccGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGacac > 1:370511/1‑71 (MQ=255)
ccGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGacac > 1:619189/1‑71 (MQ=255)
ccGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGacac > 1:2530991/1‑71 (MQ=255)
aaTCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCAt < 1:2445511/71‑1 (MQ=255)
aTCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATa < 1:495805/71‑1 (MQ=255)
ttGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTa > 1:948199/1‑71 (MQ=255)
gCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTa > 1:244175/1‑69 (MQ=255)
gCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACt > 1:240189/1‑71 (MQ=255)
ttttttAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGAtt < 1:1991354/62‑1 (MQ=255)
ttttttAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGAtt < 1:2123433/62‑1 (MQ=255)
ttttttAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGAtt < 1:2288672/62‑1 (MQ=255)
tttttAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAAt > 1:1090854/1‑71 (MQ=255)
ttttAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAAtt > 1:557967/1‑71 (MQ=255)
gtgtTCCAGCGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGa < 1:45086/51‑1 (MQ=255)
ttCCAGCGTTAATTTCCTCTTCCCGCTCAAAACGCGTGACACCATAGATTTACTGCCAATTTGCGGCAGa < 1:1047115/70‑1 (MQ=255)
ttCCAGCGTTAATTTCCTCTTCACGCTCAAAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGa < 1:41332/70‑1 (MQ=255)
cGTTAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCgg > 1:841966/1‑60 (MQ=255)
cGTTAATTTCCTCTTCCCGCTCAAAACGCGTGACAcc > 1:241835/1‑37 (MQ=255)
cGTTAATTTCCTCTTCCCGCTCAAAACGCGTGACAcc > 1:2626731/1‑37 (MQ=255)
cGTTAATTTCCTCTTCCCGCTCAAAACGCGTGACAcc > 1:1334234/1‑37 (MQ=255)
ttAATTTCCTCTTCCCGCTCAGAACGCGTGACACCATAGAttt < 1:2001719/43‑1 (MQ=255)
aaTTTCCTCTTCCCGCTCAGAACGCGTGACACCATa > 1:2750772/1‑36 (MQ=255)
tttCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAg < 1:153186/57‑1 (MQ=255)
tCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGaaa > 1:2130509/1‑63 (MQ=255)
tCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGaaa > 1:1925946/1‑63 (MQ=255)
tCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGaaa > 1:990324/1‑63 (MQ=255)
tCCTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTaaa > 1:2562329/1‑71 (MQ=255)
tCCTCTTCCCGCTCAAAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTaaa > 1:2375166/1‑71 (MQ=255)
tCCTCTTCCCGCTCAAAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTaaa > 1:1187456/1‑71 (MQ=255)
ccTCTTCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAAc > 1:2088765/1‑71 (MQ=255)
ttCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAACCata > 1:91105/1‑71 (MQ=255)
ttCCCGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAACCa < 1:1058442/69‑1 (MQ=255)
cccGCTCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAACCATAtt > 1:585531/1‑71 (MQ=255)
tCAGAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAACCATATTGATc < 1:1001190/70‑1 (MQ=255)
|
GGGAGAAATGCCGAATCGCGTTGCCAATTTTTTAGCGTGTTCCAGCGTTAATTTCCTCTTCCCGCTCAAAACGCGTGACACCATAGATTTACTGCCAATTTCCGGCAGATCGGAAAGGGTTAAACCATATTGATC > W3110S.gb/3232402‑3232536
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
