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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,334,140 |
A→G |
17.4% |
K530R (AAG→AGG) |
fdoG → |
formate dehydrogenase‑O, large subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,334,140 | 0 | A | G | 17.4%
| 97.5
/ 15.1
| 46 | K530R (AAG→AGG) | fdoG | formate dehydrogenase‑O, large subunit |
| Reads supporting (aligned to +/- strand): ref base A (24/14); new base G (2/6); total (26/20) |
| Fisher's exact test for biased strand distribution p-value = 6.25e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01 |
TGATGAAGGCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCTATAT > minE/2334074‑2334209
|
tgatgaAGGCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAg < 1:581875/68‑1 (MQ=255)
gatgaAGGCCTTCTTTGGTGATATAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAg < 1:525671/67‑1 (MQ=255)
aGGCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATa > 1:3020222/1‑69 (MQ=255)
aGGCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATa > 1:2278096/1‑69 (MQ=255)
gCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAgg > 1:3081300/1‑71 (MQ=255)
cttcttTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAgg > 1:3451874/1‑69 (MQ=255)
cttcttTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGc > 1:3008779/1‑70 (MQ=255)
ttGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTacgac > 1:602554/1‑71 (MQ=255)
ttGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTacgac > 1:1340138/1‑71 (MQ=255)
aTAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTg > 1:1701796/1‑71 (MQ=255)
tAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAGGTGGGATAAAGGCTACGACGTCCTg > 1:1633563/1‑70 (MQ=255)
tAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCt > 1:2627777/1‑69 (MQ=255)
gACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATa < 1:3571736/47‑1 (MQ=255)
gACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATa < 1:318509/47‑1 (MQ=255)
cgccggAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATAc > 1:1057142/4‑68 (MQ=255)
cggAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCt > 1:3164193/1‑58 (MQ=255)
cggAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTc > 1:555328/1‑68 (MQ=255)
cggAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTc > 1:1449265/1‑68 (MQ=255)
gAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAgat < 1:670814/71‑1 (MQ=255)
aaaTAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAgatga > 1:3167172/1‑71 (MQ=255)
aaTAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTac > 1:3622375/1‑45 (MQ=255)
aaTAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAgatgat > 1:1792938/1‑71 (MQ=255)
aTAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATaa > 1:1520643/1‑37 (MQ=255)
gCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTc > 1:1481193/1‑59 (MQ=255)
tGGGGCTTTGACTGGTTGCCGAGGTGGGATAAAGGCTACGACGTCCTGCAATACt < 1:548878/55‑1 (MQ=255)
tGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGaaa > 1:2131928/1‑69 (MQ=255)
gggCTTTGACTGGTTGCCGAGGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAaga < 1:1562738/69‑1 (MQ=255)
cTTTGACTGGTTGCCGAGGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCa < 1:2113217/71‑1 (MQ=255)
cTTTGACTGGTTGCCGAGGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCa < 1:125404/71‑1 (MQ=255)
ttGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGt < 1:3210798/37‑1 (MQ=255)
tGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAgggaag < 1:1318755/69‑4 (MQ=255)
tGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAgg > 1:3409503/1‑65 (MQ=255)
gACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGt > 1:1336331/1‑71 (MQ=255)
ggTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCg < 1:670888/45‑1 (MQ=255)
gTTGCCGAGGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAgatga < 1:2596522/50‑1 (MQ=255)
gTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAgg < 1:1102590/59‑1 (MQ=255)
gTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATg > 1:2436109/1‑71 (MQ=255)
tGCCGAGGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATgg > 1:3491262/1‑70 (MQ=255)
tGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCa < 1:3626595/66‑1 (MQ=255)
ccGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCg > 1:792308/1‑40 (MQ=255)
ccGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGatat < 1:3944576/44‑1 (MQ=255)
cGAGGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAAt < 1:3918658/65‑1 (MQ=255)
cGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCtat < 1:2383926/71‑1 (MQ=255)
cGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCtat < 1:1816337/71‑1 (MQ=255)
cGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCt < 1:66370/69‑1 (MQ=255)
gAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCtata > 1:3502804/1‑71 (MQ=255)
aaGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCTatat > 1:758476/1‑71 (MQ=255)
aaGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCTatat < 1:919219/71‑1 (MQ=255)
aGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAgat < 1:820039/40‑1 (MQ=255)
|
TGATGAAGGCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAGGCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCTATAT > minE/2334074‑2334209
|
| 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
