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 |
1,020,221 |
C→T |
50.0% |
A108T (GCC→ACC) |
uidC ← |
predicted outer membrane porin protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,020,221 | 0 | C | T | 50.0%
| ‑5.3
/ 32.5
| 38 | A108T (GCC→ACC) | uidC | predicted outer membrane porin protein |
| Reads supporting (aligned to +/- strand): ref base C (13/6); new base T (10/9); total (23/15) |
| Fisher's exact test for biased strand distribution p-value = 5.08e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTA > minE/1020180‑1020288
|
cAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCaa < 1:3393978/68‑1 (MQ=255)
aGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGa > 1:1820673/1‑69 (MQ=255)
aGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGa > 1:167682/1‑69 (MQ=255)
ttCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCg > 1:559681/1‑69 (MQ=255)
gggTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACt > 1:985651/1‑69 (MQ=255)
gggTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACt > 1:297705/1‑69 (MQ=255)
gggTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACt > 1:2033096/1‑69 (MQ=255)
gggTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACt > 1:16896/1‑69 (MQ=255)
gggTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACt > 1:1365413/1‑69 (MQ=255)
gggTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACt > 1:1160408/1‑69 (MQ=255)
ttttATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCat < 1:2130253/69‑1 (MQ=255)
tATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATc > 1:2201451/1‑69 (MQ=255)
tATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATc > 1:1614621/1‑69 (MQ=255)
tATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATc > 1:738760/1‑69 (MQ=255)
tATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATc > 1:3183658/1‑69 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCCGCAAGa > 1:492191/1‑45 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCatc > 1:82960/1‑66 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:2588953/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:2380314/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:2861695/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:2116953/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:1934397/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:1573133/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:3240520/1‑68 (MQ=255)
tttACTGCCCCCAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAGc > 1:1432956/1‑68 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:1154719/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:318584/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:2841783/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:2608729/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:2256537/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:1892261/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:1565768/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:1522804/57‑1 (MQ=255)
ccAGGGTAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTGCTCATATCAg < 1:1453888/57‑1 (MQ=255)
gCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta < 1:1382282/69‑1 (MQ=255)
gCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta < 1:726813/69‑1 (MQ=255)
gCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta < 1:869918/69‑1 (MQ=255)
gCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta < 1:1125977/69‑1 (MQ=255)
cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta > 1:2193722/1‑68 (MQ=255)
cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta > 1:2125344/1‑68 (MQ=255)
cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta > 1:1948810/1‑68 (MQ=255)
cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta > 1:1370217/1‑68 (MQ=255)
cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTta > 1:1305486/1‑68 (MQ=255)
|
CAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTA > minE/1020180‑1020288
|
| 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
