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 |
2,839,277 |
G→A |
44.1% |
A36A (GCC→GCT) |
blc ← |
outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,839,277 | 0 | G | A | 44.1%
| 8.0
/ 30.3
| 43 | A36A (GCC→GCT) | blc | outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (8/16); new base A (10/9); total (18/25) |
| Fisher's exact test for biased strand distribution p-value = 2.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
TTCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAGGAGAACTGCAGGCAACG > minE/2839223‑2839337
|
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:414954/69‑1 (MQ=255)
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:1401321/69‑1 (MQ=255)
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:1579742/69‑1 (MQ=255)
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:2478162/69‑1 (MQ=255)
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:1943089/69‑1 (MQ=255)
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:2097289/69‑1 (MQ=255)
ttCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAattatt < 1:2043164/69‑1 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:2445334/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:741569/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:542831/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:37614/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:2778911/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:2508401/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:1052550/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:237047/1‑58 (MQ=255)
cAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:2005706/1‑58 (MQ=255)
cAAAGCGGTCATAAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTc > 1:3055376/1‑58 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:1084999/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:1109339/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:481825/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:46855/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:1264958/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:2922032/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:2687725/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:1694153/68‑1 (MQ=255)
aaGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTAGCGTCGAAATTATTcac < 1:2200567/68‑1 (MQ=255)
gTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGt < 1:1457933/69‑1 (MQ=255)
gTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGt < 1:2911278/69‑1 (MQ=255)
gTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGt < 1:2229621/69‑1 (MQ=255)
cAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCg > 1:3202222/1‑47 (MQ=255)
cAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTcactc < 1:2617586/69‑3 (MQ=255)
cAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTcacgc > 1:2551526/1‑69 (MQ=255)
cAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTcacgc > 1:2586510/1‑69 (MQ=255)
cAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTcacgc > 1:2178459/1‑69 (MQ=255)
ctcATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGt < 1:2532340/69‑1 (MQ=255)
tcATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGt > 1:1431083/1‑68 (MQ=255)
aCCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAGGAGAACTGc > 1:2007241/1‑68 (MQ=255)
aCCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAGGAGAACTGCa > 1:660216/1‑69 (MQ=255)
aCGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAg < 1:2001754/50‑1 (MQ=255)
aCGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAg < 1:3318107/50‑1 (MQ=255)
aCGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAg < 1:2489938/50‑1 (MQ=255)
aCGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAg < 1:1572475/50‑1 (MQ=255)
aCGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAGGAGAACTGCAGGCAACg > 1:1870449/1‑67 (MQ=255)
|
TTCAAAGCGGTGATCAAAACGGGCAATCTCATACCAGGTACCGAGATAACGTTTGGCGTCGAAATTATTTACTACGGTCACGCCACGCGGCGGCGTAGGAGAACTGCAGGCAACG > minE/2839223‑2839337
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
