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 |
2,021,534 |
C→T |
31.8% |
L50L (CTA→TTA) |
yqhH → |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,021,534 | 0 | C | T | 31.8%
| 59.9
/ 32.3
| 69 | L50L (CTA→TTA) | yqhH | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base C (21/26); new base T (10/12); total (31/38) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.14e-01 |
TCAGCTGGCGAGCAATGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATACGCGTCTTGATG > minE/2021467‑2021594
|
tCAGCTGGCGAGCAATGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCAc < 1:3049157/68‑1 (MQ=255)
aaTGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATc < 1:100274/69‑1 (MQ=255)
aaTGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATc < 1:2334821/69‑1 (MQ=255)
aaTGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATc < 1:186269/69‑1 (MQ=255)
aaTGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATc < 1:925835/69‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:858743/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:1710720/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:1680901/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:3396853/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:2709777/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:2609416/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:2448359/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:1488843/68‑1 (MQ=255)
cAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTAtgc < 1:1567118/68‑1 (MQ=255)
aCATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATc < 1:414580/60‑1 (MQ=255)
aTTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCaa > 1:626152/1‑69 (MQ=255)
aTTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCaa > 1:1590787/1‑69 (MQ=255)
tAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCaaa > 1:1561758/1‑68 (MQ=255)
tAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:1557659/1‑69 (MQ=255)
tAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:1434051/1‑69 (MQ=255)
tAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:131184/1‑69 (MQ=255)
tAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:3226336/1‑69 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:1973555/1‑68 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:51673/1‑68 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:3083608/1‑68 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:1231865/1‑68 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:1401757/1‑68 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:1408898/1‑68 (MQ=255)
aaaTGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAAt > 1:141162/1‑68 (MQ=255)
tGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGa > 1:2810713/1‑69 (MQ=255)
tGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGa > 1:1262236/1‑69 (MQ=255)
tGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGa > 1:147968/1‑69 (MQ=255)
tGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGa > 1:2400602/1‑69 (MQ=255)
tGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGa > 1:2477939/1‑69 (MQ=255)
tGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGa > 1:2529273/1‑69 (MQ=255)
aaaaTCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCt < 1:624565/69‑1 (MQ=255)
aaaaTCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCt < 1:1216068/69‑1 (MQ=255)
aaaaTCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCt < 1:898023/69‑1 (MQ=255)
cGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGcc < 1:165543/69‑1 (MQ=255)
cGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGcc < 1:2901352/69‑1 (MQ=255)
ggCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGcc < 1:2159042/68‑1 (MQ=255)
ggCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGcc < 1:2831334/68‑1 (MQ=255)
gCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCaa < 1:2155590/69‑1 (MQ=255)
gCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCaa < 1:1181167/69‑1 (MQ=255)
cTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCaa < 1:3246526/68‑1 (MQ=255)
ttGAGCAGGATATGAAAGCACTACGCCCACAAATc < 1:169124/35‑1 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCt > 1:1336397/1‑35 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:377683/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:994868/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:2774427/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:276292/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:1417110/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:1915895/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:1895361/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATAc > 1:1866695/1‑69 (MQ=255)
tGAGCAGGATATGAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCAAATAc > 1:831295/1‑69 (MQ=255)
ggATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATACGCGTc > 1:2978410/1‑68 (MQ=255)
tGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATACGCGGCTTGATg < 1:3017837/69‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:1020627/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:956554/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:1099055/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:1862001/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:698518/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:486310/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:478261/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:2721396/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:2754435/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:275985/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:3236548/44‑1 (MQ=255)
gAAAGCATTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTa < 1:3133651/44‑1 (MQ=255)
|
TCAGCTGGCGAGCAATGTGCAAACATTAAATGCCAAAATCGCCCGGCTTGAGCAGGATATGAAAGCACTACGCCCACAAATCTATGCTGCCAAATCCGAAGCTAACAGAGCCAATACGCGTCTTGATG > minE/2021467‑2021594
|
| 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
