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 |
894,163 |
C→T |
14.3% |
A88T (GCG→ACG) |
sapB ← |
predicted antimicrobial peptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 894,163 | 0 | C | T | 14.3%
| 136.3
/ 9.2
| 76 | A88T (GCG→ACG) | sapB | predicted antimicrobial peptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (38/27); new base T (9/2); total (47/29) |
| Fisher's exact test for biased strand distribution p-value = 1.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 |
ATCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCTTTTAACTGTTCGGCAATC > minE/894101‑894230
|
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaacc > 1:2910308/1‑66 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaaa > 1:2237765/1‑67 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:1075181/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:1803912/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:1286452/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:2427301/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:1402650/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:78799/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:74048/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:3372469/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:1517790/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCaaa < 1:2937663/66‑1 (MQ=255)
aTCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAAc > 1:106047/1‑68 (MQ=255)
cTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg < 1:1489899/69‑1 (MQ=255)
cTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg < 1:834653/69‑1 (MQ=255)
cTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg < 1:2891229/69‑1 (MQ=255)
cTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg < 1:2892379/69‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:43549/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:2450244/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:2817228/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:368160/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:230931/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:2305762/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:2099940/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:641223/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:1479444/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:760377/68‑1 (MQ=255)
ggCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:774114/68‑1 (MQ=255)
gcgcGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:814203/67‑1 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCa > 1:1565437/1‑68 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:1040751/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:973453/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:2859904/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:3064458/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:3378718/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:1734385/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:1790362/1‑69 (MQ=255)
cccGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCAt > 1:2275305/1‑69 (MQ=255)
catcTCCACGGGGATGCCAACAATCAGCGCAAAACC‑AAGGCGAg > 1:1025443/1‑44 (MQ=38)
catcCCCACGGGGATGCCAACAATCAGCGCGAAACCGAAGGCGAg > 1:374517/1‑45 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg > 1:3015428/1‑45 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg > 1:28775/1‑45 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg > 1:1547971/1‑45 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAg > 1:2527180/1‑45 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATGGTCGCCg > 1:699542/1‑68 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:1680610/1‑68 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:1635906/1‑68 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:821171/1‑68 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:1312184/1‑68 (MQ=255)
catcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:1415090/1‑68 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:498958/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:1364549/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:408428/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:2352337/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:3299518/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:3127656/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:3062418/1‑67 (MQ=255)
atcCCCACGGGGATGCCAACAATCAGCGCAAAACAGAAGGCGAGGATGCACAGTTCCATCGTCGCCg > 1:2736191/1‑67 (MQ=255)
ccccACGGGGATGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGaa < 1:2886087/69‑1 (MQ=255)
ccccACGGGGATGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGaa < 1:3148758/69‑1 (MQ=255)
cccACGGGGATGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:2616569/1‑69 (MQ=255)
cccACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:832594/1‑69 (MQ=255)
cccACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:1225864/1‑69 (MQ=255)
cccACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:2913564/1‑69 (MQ=255)
cccACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:60869/1‑69 (MQ=255)
cccACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:515161/1‑69 (MQ=255)
cccACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAg > 1:2059988/1‑69 (MQ=255)
cGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATg < 1:2637222/41‑1 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGaa > 1:546310/1‑59 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGATCTCtttt > 1:594484/1‑69 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCtttt > 1:652643/1‑69 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCtttt > 1:247236/1‑69 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCtttt > 1:3363225/1‑69 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCtttt > 1:973975/1‑69 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCttt > 1:1748865/1‑68 (MQ=255)
aTGCCAACAATCAGCGTAAAACCGAAGACGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCtttt > 1:765167/1‑69 (MQ=255)
gcAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCTTTTAACTGTTCGGCAATc > 1:1874474/1‑69 (MQ=255)
|
ATCCTGCCACTTATGGCGCGTAATCCCGGCAATCATCCCCACGGGGATGCCAACAATCAGCGCAAAACCGAAGGCGAGGATGCACAGTTCCATCGTCGCCGGGAAGACCTCTTTTAACTGTTCGGCAATC > minE/894101‑894230
|
| 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
