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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,047,977 |
G→A |
34.6% |
P137P (CCG→CCA) |
slyB → |
outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,047,977 | 0 | G | A | 34.6%
| 55.3
/ 40.6
| 75 | P137P (CCG→CCA) | slyB | outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (5/44); new base A (12/14); total (17/58) |
| Fisher's exact test for biased strand distribution p-value = 9.20e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01 |
AAAGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGTTT > minE/1047918‑1048023
|
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:1167824/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:2777515/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:2541163/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:2460056/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:2019386/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:1420448/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:1301691/68‑1 (MQ=255)
aaaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:1222429/68‑1 (MQ=255)
aaGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:2038847/67‑1 (MQ=255)
aCGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCg < 1:2384381/69‑1 (MQ=255)
aCGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCg < 1:1307592/69‑1 (MQ=255)
aCGAAGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCg < 1:3341873/69‑1 (MQ=255)
tACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACg < 1:3366544/54‑1 (MQ=255)
aCCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCg > 1:3166553/1‑45 (MQ=255)
aCCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc > 1:994596/1‑69 (MQ=255)
aCCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:1588832/69‑1 (MQ=255)
aCCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc > 1:976749/1‑69 (MQ=255)
atGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:3218283/63‑1 (MQ=255)
atGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc > 1:2860554/1‑63 (MQ=255)
atGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:893469/63‑1 (MQ=255)
atGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:2028020/63‑1 (MQ=255)
atGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:964336/63‑1 (MQ=255)
atGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:3050132/63‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:963189/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:2167769/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:286018/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:784556/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:292105/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:296489/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:2571318/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:3278552/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:571804/69‑1 (MQ=255)
ggtACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:2423919/69‑1 (MQ=255)
tACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAg > 1:135164/1‑68 (MQ=255)
tACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAg > 1:49654/1‑68 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGc < 1:836115/54‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:588202/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:47708/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:2287873/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:1336556/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:456044/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:2270246/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:818521/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:1646707/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:1670113/69‑1 (MQ=255)
cAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAAAGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:1504396/69‑1 (MQ=255)
aCAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGt < 1:2283080/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCATGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:2459044/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:965847/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:3314204/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:740114/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:1376667/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:3176445/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:1836223/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:1919789/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:1983361/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:2414769/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:2348197/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:2105808/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:2187973/69‑1 (MQ=255)
aaGGGAACACTCATTTCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGttt < 1:2214172/69‑1 (MQ=255)
cacTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:2312861/51‑1 (MQ=255)
acTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCa < 1:2773606/50‑1 (MQ=255)
ttCTCTCCAGGCCATCGTGTCGTACTGGCCAGCAAt > 1:199913/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:3091009/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:929651/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:2090472/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:228733/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:678966/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:614654/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:2480778/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:1061064/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:3354917/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:2793466/1‑36 (MQ=255)
ttCTCTCCAGGCCAACGTGTCGTACTGGCCAGCAAt > 1:2917738/1‑36 (MQ=255)
cGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTg < 1:1403874/41‑1 (MQ=255)
|
AAAGACGATGGTAATACCATCATGGTGGTACAGAAACAAGGCAACACTCGTTTCTCTCCGGGCCAACGTGTCGTACTGGCCAGCAATGGCAGTCAGGTGACCGTTT > minE/1047918‑1048023
|
| 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
