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 |
304,408 |
T→A |
32.6% |
P187P (CCT→CCA) |
ybaY → |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 304,408 | 0 | T | A | 32.6%
| 48.0
/ 33.8
| 49 | P187P (CCT→CCA) | ybaY | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base T (10/23); new base A (11/5); total (21/28) |
| Fisher's exact test for biased strand distribution p-value = 1.51e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01 |
CAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGATAACGCTGCA > minE/304344‑304476
|
cAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGc < 1:2037837/69‑1 (MQ=255)
cAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGc < 1:502388/69‑1 (MQ=255)
cAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGc < 1:2836494/69‑1 (MQ=255)
cAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGc < 1:3300741/69‑1 (MQ=255)
cAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGc < 1:1789134/69‑1 (MQ=255)
cAACGACTACCGTACCTTCGACTTCACCAACTCAGGGGAATCCGTCTTCGGCAGTTCCAGCTCCTACGc < 1:1446429/69‑1 (MQ=255)
aCGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCaa > 1:905994/1‑69 (MQ=255)
aCGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCaa > 1:3268499/1‑69 (MQ=255)
aCGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCaa > 1:1421706/1‑69 (MQ=255)
ccTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGa > 1:3206360/1‑67 (MQ=255)
ccTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGa > 1:2106871/1‑67 (MQ=255)
ccTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGa > 1:2889978/1‑67 (MQ=255)
ccTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGAc > 1:642791/1‑68 (MQ=255)
aCTTCACCAACCCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTaa < 1:2229039/67‑1 (MQ=255)
aCTTCACCAACCCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTaa < 1:1836926/67‑1 (MQ=255)
aCTTCACCAACCCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTaa < 1:2888222/67‑1 (MQ=255)
aCTTCACCAACCCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTaa < 1:2101113/67‑1 (MQ=255)
gTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGga < 1:2275127/67‑1 (MQ=255)
gTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGga < 1:1102567/67‑1 (MQ=255)
gTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGga < 1:1952668/67‑1 (MQ=255)
gTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGga < 1:1785254/67‑1 (MQ=255)
gTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGga < 1:91973/67‑1 (MQ=255)
gTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGga < 1:1168919/67‑1 (MQ=255)
aTCCGTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTaa < 1:2490006/48‑1 (MQ=255)
tCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTaa > 1:350223/1‑47 (MQ=255)
tCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCg > 1:563775/1‑60 (MQ=255)
tCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCg > 1:2922158/1‑60 (MQ=255)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCg > 1:423436/1‑37 (MQ=255)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCg > 1:1581327/1‑37 (MQ=255)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCg > 1:1169175/1‑37 (MQ=255)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGt > 1:2647194/1‑41 (MQ=38)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:821594/1‑69 (MQ=39)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:2509420/1‑69 (MQ=39)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:2931083/1‑69 (MQ=39)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:1317365/1‑69 (MQ=39)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:2535327/1‑69 (MQ=39)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:1907846/1‑69 (MQ=39)
gTCTTCGGCAGTTCCAGCTCCAACGCAATATTAAGCGAAGTTAACCCTCTCCGCCCGGAGAGGGTtagt > 1:239282/1‑69 (MQ=39)
tCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTtagt < 1:3010772/68‑1 (MQ=255)
tCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTtagt < 1:1193829/68‑1 (MQ=255)
tCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTtagt < 1:787635/68‑1 (MQ=255)
tCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTtagt < 1:461188/68‑1 (MQ=255)
tCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTtagt < 1:2412281/68‑1 (MQ=255)
tCTTCGGCAGGTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTtagt < 1:3250199/68‑1 (MQ=255)
tCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGAt < 1:1713562/69‑1 (MQ=255)
tCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGAt < 1:1616885/69‑1 (MQ=255)
tCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGAt < 1:1012051/69‑1 (MQ=255)
tCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGAt < 1:2896846/69‑1 (MQ=255)
tCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGAt < 1:950496/69‑1 (MQ=255)
tACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGATAACGCTGCa > 1:1240375/1‑69 (MQ=255)
|
CAACGACTACCGTACCTTCGACTTCACCAACTCAGGTGAATCCGTCTTCGGCAGTTCCAGCTCCTACGCAATATTAAGCGACGTTAACCCTCTCCGCCCGGAGAGGGTTAGTAGTTCCAGCGATAACGCTGCA > minE/304344‑304476
|
| 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
