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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
974,262:1 |
+C |
62.0% |
intergenic (+14/+978) |
lsrB → / ← ydeH |
AI2 transporter/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 974,262 | 1 | . | C | 62.0%
| 103.3
/ 63.6
| 50 | intergenic (+14/+978) | lsrB/ydeH | AI2 transporter/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (11/8); new base C (20/11); total (31/19) |
| Fisher's exact test for biased strand distribution p-value = 7.66e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-01 |
CTGTTACCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGCCTTCGTTTAGGTTA > minE/974192‑974331
|
cTGTTACCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTaa > 1:1987681/1‑71 (MQ=255)
ttACCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑c < 1:1463969/69‑1 (MQ=255)
tACCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑ccg > 1:4434192/1‑68 (MQ=255)
tACCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑Cgg < 1:1397071/70‑1 (MQ=255)
aCCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑ccg > 1:1866785/1‑67 (MQ=255)
aGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAg > 1:2233049/1‑71 (MQ=255)
aGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGt < 1:5478875/71‑1 (MQ=255)
gcgcGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGt < 1:4847093/71‑1 (MQ=255)
gcgcGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGt < 1:5131252/71‑1 (MQ=255)
gcgcGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGt < 1:1798184/71‑1 (MQ=255)
cgcgTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTa < 1:4265872/71‑1 (MQ=255)
cgTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa < 1:691835/70‑1 (MQ=255)
gATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATgg > 1:3431385/1‑69 (MQ=255)
atatTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATgg > 1:5247865/1‑69 (MQ=255)
atatTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATgg > 1:1231815/1‑69 (MQ=255)
atTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATgg > 1:5595656/1‑67 (MQ=255)
atTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTa > 1:1181174/1‑63 (MQ=255)
atTCAACAAAGAGAATATCGGCAAATACGATATCTGATGTGCATTACTTAACCGGAGTAAGTTATgg > 1:4075056/1‑67 (MQ=255)
ttCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgat > 1:5347349/1‑71 (MQ=255)
ttCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgat > 1:3176052/1‑71 (MQ=255)
tCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCTGAGTAAGTTATGGCAgatt > 1:3805578/1‑70 (MQ=255)
caacaaAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATGGCAgatgat > 1:591425/1‑71 (MQ=255)
aacaaAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgattta < 1:3658627/71‑4 (MQ=255)
aacaaAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgattta < 1:1515605/71‑4 (MQ=255)
acaaAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:2978942/1‑59 (MQ=255)
acaaAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑cc > 1:4158322/1‑47 (MQ=255)
caaAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGt < 1:3068304/56‑1 (MQ=255)
aaGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:149690/1‑56 (MQ=255)
aaGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGGAgatt < 1:2215434/65‑2 (MQ=255)
aaGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgatt < 1:3430182/65‑2 (MQ=255)
aaGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgatt < 1:1871171/65‑2 (MQ=255)
aaGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGt < 1:1128438/53‑1 (MQ=255)
aaGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATgg < 1:1567293/58‑1 (MQ=255)
agagAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAg > 1:4754353/1‑70 (MQ=255)
gaATATCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATGGCAgatt < 1:5164537/61‑2 (MQ=255)
aaTATCGGCAAATACGATTTCTGATGTGCATTACTTaa > 1:3200052/1‑38 (MQ=255)
aaTATCGGCAAATACGATTTCTGATGTGCATTACTTaa > 1:5411579/1‑38 (MQ=255)
atatCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATg > 1:1380248/1‑52 (MQ=255)
tCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:155168/1‑47 (MQ=255)
tCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:5371117/1‑47 (MQ=255)
tCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:2303256/1‑47 (MQ=255)
tCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:2463338/1‑47 (MQ=255)
tCGGCAAATACGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:4425393/1‑47 (MQ=255)
cGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTAt > 1:2413304/1‑46 (MQ=255)
cGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTAt > 1:555413/1‑46 (MQ=255)
cGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTAt > 1:2612220/1‑46 (MQ=255)
cGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTAt > 1:3935288/1‑46 (MQ=255)
cGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:1416214/1‑37 (MQ=38)
cGATTTCTGATGTGCATTACTTAACCGGAGTAAGTTa > 1:3701417/1‑37 (MQ=38)
gATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATg > 1:951275/1‑38 (MQ=37)
gATTTCTGATGTGCATTACTTAACCGGAGTAAGTTATg > 1:1728679/1‑38 (MQ=37)
gATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTa < 1:5613460/71‑1 (MQ=255)
tGATGTGCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAg > 1:5099383/1‑71 (MQ=255)
aTGTGCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGcc < 1:2479501/71‑1 (MQ=255)
gtgCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGCCtt > 1:724949/1‑71 (MQ=255)
aTTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGCCTTCGtt < 1:1120900/71‑1 (MQ=255)
ttACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGCCTTCGtt > 1:284610/1‑70 (MQ=255)
a‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGCCTTCGTTTAGGTTa < 1:712448/70‑1 (MQ=255)
|
CTGTTACCGGAGCGCGTGATATTCAACAAAGAGAATATCGGCAAATACGATTTCTGATGTGCATTACTTAA‑CGGAGTAAGTTATGGCAGATGATTTAAGTCGAACACAATAAAGATTTAATTCAGCCTTCGTTTAGGTTA > minE/974192‑974331
|
| 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
