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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,608,096 |
T→C |
35.6% |
intergenic (‑206/+104) |
pitA ← / ← nikR |
phosphate transporter, low‑affinity/DNA‑binding transcriptional regulator, Ni‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,608,096 | 0 | T | C | 35.6%
| 35.1
/ 38.8
| 45 | intergenic (‑206/+104) | pitA/nikR | phosphate transporter, low‑affinity/DNA‑binding transcriptional regulator, Ni‑binding |
| Reads supporting (aligned to +/- strand): ref base T (15/14); new base C (11/5); total (26/19) |
| Fisher's exact test for biased strand distribution p-value = 3.51e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.75e-01 |
TCAGGCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGCCCTT > minE/2608028‑2608165
|
tCAGGCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGccc > 1:3930310/1‑71 (MQ=255)
cAGGCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCg > 1:1374382/1‑71 (MQ=255)
cAGGCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCg > 1:857431/1‑71 (MQ=255)
cAGGCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCg > 1:1915611/1‑71 (MQ=255)
ggCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGtt > 1:3893897/1‑71 (MQ=255)
aaaTACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGttttt > 1:644422/1‑71 (MQ=255)
aTACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGtttttt > 1:4923204/1‑70 (MQ=255)
aTACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGtttttt > 1:2118391/1‑70 (MQ=255)
tACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGtttttt‑t > 1:4453845/1‑70 (MQ=255)
tACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGtttttt > 1:403954/1‑69 (MQ=255)
tACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑Ta < 1:4770038/71‑1 (MQ=255)
ccTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAaga < 1:3109219/69‑1 (MQ=255)
ccTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAagag > 1:305275/1‑71 (MQ=255)
ccTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAaga < 1:673437/70‑1 (MQ=255)
atatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTc > 1:3669960/1‑71 (MQ=255)
atatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAaga > 1:4937412/1‑60 (MQ=255)
atatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAAcg > 1:4228536/1‑70 (MQ=255)
atatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAAcg > 1:631526/1‑70 (MQ=255)
tatTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCg < 1:2676509/71‑1 (MQ=255)
ttGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:5236651/1‑71 (MQ=255)
ttGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:1057640/1‑71 (MQ=255)
ttGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAAcgtg < 1:2997344/70‑4 (MQ=255)
gATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:2577980/1‑69 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAaga < 1:4810235/47‑1 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAaga < 1:874692/47‑1 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAaga < 1:3617268/47‑1 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTAtt < 1:2300249/71‑1 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAACGTGGAAAggttt > 1:2578678/1‑67 (MQ=255)
gTGCGACCACTGAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAACGTGGAAAggttt < 1:4867585/70‑4 (MQ=255)
gACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTaga < 1:5421076/71‑1 (MQ=255)
gACCACTGAGGAATCTTTACAATTCAAGCCCGTTTTTTCTAAgagga < 1:4595341/47‑1 (MQ=255)
ccACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTagaga < 1:485510/71‑1 (MQ=255)
tGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATa < 1:5499600/54‑1 (MQ=255)
tGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATa < 1:64158/54‑1 (MQ=255)
tGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATa < 1:1322613/54‑1 (MQ=255)
gAGGAATCTTTACAATTCACGCCCGTTTTTTCTAAGAGGAGCGCAACGTGGAAAggtt > 1:1562825/1‑56 (MQ=255)
aTCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:3811757/1‑46 (MQ=255)
aTCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:5631197/1‑46 (MQ=255)
aTCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGa > 1:827686/1‑46 (MQ=255)
cTTTACAATTCACGCCCGTTTTTTCTAAGAGGAgcgc < 1:3927858/37‑1 (MQ=255)
tttACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCaa < 1:3927597/37‑1 (MQ=255)
tttACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCaa < 1:1736691/37‑1 (MQ=255)
ttACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGc > 1:3951402/1‑71 (MQ=255)
cACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGcc > 1:4621154/1‑71 (MQ=255)
cACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGcc > 1:815398/1‑71 (MQ=255)
gTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGCCCtt > 1:3232550/1‑71 (MQ=255)
|
TCAGGCAAATACTTCCTTTTAGTAATATTGATGCTGGTGCGACCACTGAGGAATCTTTACAATTCACGTCCGTTTTTT‑TAAGAGGAGCGCAACTCGGATAGGGTATTTAGAGAGGAATCAGGTGTGCTAGTGGCCCTT > minE/2608028‑2608165
|
| 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
