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 |
1,446,895 |
G→A |
45.4% |
I162I (ATC→ATT) |
rcsC ← |
hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,446,895 | 0 | G | A | 45.4%
| 5.2
/ 32.8
| 44 | I162I (ATC→ATT) | rcsC | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| Reads supporting (aligned to +/- strand): ref base G (12/12); new base A (3/17); total (15/29) |
| Fisher's exact test for biased strand distribution p-value = 2.46e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01 |
TTCGCTGATCCAGTAGAGGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAT > minE/1446835‑1446959
|
ttCGCTGATCCAGTAGAGGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGt > 1:869043/1‑67 (MQ=255)
ttCGCTGATCCAGTAGAGGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTc > 1:890654/1‑69 (MQ=255)
ttCGCTGATCCAGTAGAGGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTc > 1:1138324/1‑69 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGGGTTCATGCAAAGc < 1:2814878/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:112575/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:765926/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:605103/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:3329220/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:3206344/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:3197643/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2940343/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2641809/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2639769/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2410612/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2241628/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:1468416/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:1042043/69‑1 (MQ=255)
ccAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2142044/69‑1 (MQ=255)
cAGTAGAGGTTACTGCCACTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:762645/68‑1 (MQ=255)
gagGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCaa > 1:326980/1‑69 (MQ=255)
gagGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCaa > 1:2028747/1‑69 (MQ=255)
tACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCgg > 1:81750/1‑69 (MQ=255)
ccacTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGCTTTTAGCGCGGTATcg > 1:257754/4‑69 (MQ=255)
ccacTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGCTTTTAGCGCGGTATcg > 1:2967954/4‑69 (MQ=255)
ccacTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGCTTTTAGCGCGGTATcg > 1:660573/4‑69 (MQ=255)
acTATCATCTTGTGGTGCATTTCGATATTTATTAATGCGTTCATGCAAAGc < 1:2367793/50‑1 (MQ=255)
atcatcTTGTGGTGCATTTCGATATTTATTGATGCGTTCATTCAAAGCTTTCAACGCGGTATCGCGTTc < 1:387167/69‑1 (MQ=255)
atcatcTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTc < 1:262971/69‑1 (MQ=255)
atcatcTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTc < 1:1632747/69‑1 (MQ=255)
atcTTGTGGTGCATTTCGATATTTATTGATGCGtt < 1:2132794/35‑1 (MQ=255)
atcTTGTGGTGCATTTCGATATTTATTGATGCGtt < 1:2220185/35‑1 (MQ=255)
ggtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCa < 1:1377598/67‑1 (MQ=255)
ggtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCa < 1:679354/67‑1 (MQ=255)
ggtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCa < 1:1544184/67‑1 (MQ=255)
tttCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACg < 1:2265205/68‑1 (MQ=255)
tttCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACg < 1:2217886/68‑1 (MQ=255)
tCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGt < 1:453586/42‑1 (MQ=255)
tCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGt < 1:898782/42‑1 (MQ=255)
tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACTGAAAt > 1:2834587/1‑69 (MQ=255)
tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAt > 1:164158/1‑69 (MQ=255)
tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAt > 1:1783441/1‑69 (MQ=255)
tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAt > 1:273225/1‑69 (MQ=255)
tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAt > 1:971666/1‑69 (MQ=255)
tattGATGCGTTCATGAAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAt > 1:1458808/1‑69 (MQ=255)
|
TTCGCTGATCCAGTAGAGGTTACTGCCGCTATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAAT > minE/1446835‑1446959
|
| 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
