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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,069,625 |
C→T |
10.4% |
intergenic (‑167/‑1147) |
insH ← / → yoeA |
IS5 transposase and trans‑activator/CP4‑44 prophage region; ECK1989:JW5326:b1995; predicted disrupted hemin or colicin receptor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,069,625 | 0 | C | T | 10.4%
| 143.2
/ 6.5
| 48 | intergenic (‑167/‑1147) | insH/yoeA | IS5 transposase and trans‑activator/CP4‑44 prophage region; ECK1989:JW5326:b1995; predicted disrupted hemin or colicin receptor |
| Reads supporting (aligned to +/- strand): ref base C (25/18); new base T (3/2); total (28/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01 |
TTTATTAGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTCAGCAGGCGGGAT > W3110S.gb/2069561‑2069691
|
tttATTAGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCg > 1:3063494/1‑68 (MQ=255)
tttATTAGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCg > 1:3280980/1‑68 (MQ=255)
ttattaGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCt > 1:3241814/1‑69 (MQ=255)
ttattaGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCt > 1:2730772/1‑69 (MQ=255)
ttattaGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCt < 1:1975983/69‑1 (MQ=255)
accaGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACAtcatca > 1:2056556/1‑68 (MQ=255)
aGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGa > 1:1499847/1‑68 (MQ=255)
gTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCAtcttct < 1:2093805/47‑1 (MQ=255)
gTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATa > 1:196483/1‑67 (MQ=255)
tAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACatcatc < 1:2706222/57‑1 (MQ=255)
tAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAg > 1:1518238/1‑69 (MQ=255)
aCCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAgg < 1:2813024/68‑1 (MQ=255)
aCCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAgg < 1:2773962/68‑1 (MQ=255)
ggTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTAt > 1:1757442/1‑69 (MQ=255)
gTAACCACGACCCAGTCGGGGATATATTCCATCTTTTCGCTGACATCATCAAGAATAAAAAGGTTTAt > 1:2813623/1‑68 (MQ=255)
gTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATaaa > 1:57862/1‑59 (MQ=255)
gTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATaaa > 1:2696552/1‑59 (MQ=255)
gTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATaaa > 1:3410035/1‑59 (MQ=255)
gTAACCACGACCCAGTCGGGGATATACTCCATCTTCTCGCTGACATCATCAAGAATaa > 1:1614191/1‑58 (MQ=255)
tAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATaaa < 1:1430570/58‑1 (MQ=255)
ccACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATaaa < 1:1476517/55‑1 (MQ=255)
cACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTa < 1:2323638/62‑1 (MQ=255)
cACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATcac < 1:653583/66‑1 (MQ=255)
cACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATcac < 1:3531431/66‑1 (MQ=255)
cACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATcac < 1:2092822/66‑1 (MQ=255)
cACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATcac < 1:1300394/66‑1 (MQ=255)
aGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCaa > 1:2110000/1‑69 (MQ=255)
aGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCaa > 1:3418446/1‑69 (MQ=255)
cGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATaaaaa > 1:2547497/1‑45 (MQ=255)
ggggATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCag > 1:2076712/1‑60 (MQ=255)
ggggATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCag > 1:265352/1‑60 (MQ=255)
ggATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGttc < 1:1703753/68‑1 (MQ=255)
tatatTCAATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACg > 1:43588/1‑62 (MQ=255)
atatTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcag < 1:207499/69‑1 (MQ=255)
atatTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcag < 1:3625286/69‑1 (MQ=255)
tatTCCATCTTTTCGCTGACATCATCAAGAATAAAAAgg < 1:3465810/39‑1 (MQ=255)
tatTCCATCTTTTCGCTGACATCATCAAGAATAAAAAgg < 1:3321367/39‑1 (MQ=255)
tatTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcagc > 1:1553582/1‑69 (MQ=255)
tatTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcagc > 1:152518/1‑69 (MQ=255)
atTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcagca > 1:1709064/1‑69 (MQ=255)
atTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcagca > 1:787876/1‑69 (MQ=255)
ttCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGt > 1:2608534/1‑38 (MQ=255)
ttCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcagcag > 1:3277834/1‑69 (MQ=255)
tCCATCTTTTCGCTGACATCATCAAGAATAAAAAGGTTTATCacac > 1:1530778/1‑46 (MQ=255)
tCCATCTTTTCGCTGACATCATCAAGAATAAAAAGGTTTATCacac > 1:797081/1‑46 (MQ=255)
ccATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcag < 1:2108029/64‑1 (MQ=255)
ccATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcag < 1:2578917/64‑1 (MQ=255)
ccATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcag < 1:7877/64‑1 (MQ=255)
ccATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTcag < 1:1016664/64‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACt < 1:1255548/41‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACt < 1:849894/41‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACt < 1:468777/41‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACt < 1:2792164/41‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACt < 1:2014693/41‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACt < 1:1832421/41‑1 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTCAGCAGGCGGGAt > 1:1524639/1‑69 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTCAGCAGGCGGGAt > 1:151206/1‑69 (MQ=255)
ttctCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTCAGCAGGCGGGAt > 1:937062/1‑69 (MQ=255)
|
TTTATTAGCGCCACCAGATGTTTAACCGGGTAACCACGACCCAGTCGGGGATATATTCCATCTTCTCGCTGACATCATCAAGAATAAAAAGGTTTATCACACTCAGAGCAACGTTCTTCAGCAGGCGGGAT > W3110S.gb/2069561‑2069691
|
| 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
