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 |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,815,914 |
T→C |
82.6% |
N702D (AAT→GAT) |
spoT ← |
bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,815,914 | 0 | T | C | 82.6%
| 110.6
/ 14.9
| 46 | N702D (AAT→GAT) | spoT | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| Reads supporting (aligned to +/- strand): ref base T (6/2); new base C (16/22); total (22/24) |
| Fisher's exact test for biased strand distribution p-value = 1.28e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCAGATG > W3110S.gb/3815848‑3815980
|
cAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttc > 1:631748/1‑69 (MQ=255)
cAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtctc > 1:3035523/1‑69 (MQ=255)
cAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtctc > 1:3348038/1‑69 (MQ=255)
cAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtctc > 1:2156618/1‑69 (MQ=255)
cAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtctc > 1:2198013/1‑69 (MQ=255)
cAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtctc > 1:2491131/1‑69 (MQ=255)
ggCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCGTAAAACATTAAtttcgg > 1:291257/1‑69 (MQ=255)
gccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCggg < 1:1268273/69‑1 (MQ=255)
gccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCggg < 1:3563388/69‑1 (MQ=255)
aGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTa < 1:837808/69‑1 (MQ=255)
aGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTa < 1:1952955/69‑1 (MQ=255)
aGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTa < 1:3171509/69‑1 (MQ=255)
gCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTa < 1:561146/68‑1 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg > 1:980313/1‑69 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg > 1:2663784/1‑69 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg > 1:3404082/1‑69 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg > 1:431332/1‑69 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt > 1:2133706/1‑69 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt > 1:2978902/1‑69 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCAcg > 1:209652/1‑68 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACttt > 1:2091781/1‑49 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCAcg > 1:537793/1‑68 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCAcg > 1:3257379/1‑68 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCAcg > 1:1080965/1‑68 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCAcg > 1:1286970/1‑68 (MQ=255)
cATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTAAATCACGTCTGGCATCAcg > 1:3313651/1‑68 (MQ=255)
aCGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGAt > 1:1714637/1‑69 (MQ=255)
gtgtTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGAtt < 1:1056323/68‑1 (MQ=255)
gtgtTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGAtt < 1:2732921/68‑1 (MQ=255)
gggTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg < 1:748089/45‑1 (MQ=255)
gggTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg < 1:2166795/45‑1 (MQ=255)
gggTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg < 1:2460044/45‑1 (MQ=255)
gggTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTgcg < 1:912048/68‑1 (MQ=255)
ttCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCAt < 1:2936484/68‑1 (MQ=255)
ttCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCAt < 1:718839/68‑1 (MQ=255)
ttCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCAt < 1:2766642/68‑1 (MQ=255)
tCATAAAACATTAATTTCGGTTTCGGGTGACTTTaa < 1:799064/36‑1 (MQ=255)
tCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACg < 1:1319233/41‑1 (MQ=255)
tCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGa > 1:683018/1‑69 (MQ=255)
cATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:947142/1‑69 (MQ=255)
aaaCATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:2971227/1‑65 (MQ=255)
aaaCATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTc > 1:3685568/1‑69 (MQ=255)
aaaCATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTc > 1:2679624/1‑69 (MQ=255)
aaaCATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTc > 1:3328325/1‑69 (MQ=255)
aCATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTc > 1:711844/1‑67 (MQ=255)
aCATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTc > 1:3172288/1‑67 (MQ=255)
aTTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCa < 1:3177787/69‑1 (MQ=255)
aTTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCa < 1:3727924/69‑1 (MQ=255)
aTTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCa < 1:886655/69‑1 (MQ=255)
aTTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCa < 1:3669946/69‑1 (MQ=255)
ttAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCAg < 1:3387822/69‑1 (MQ=255)
ttAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCAg < 1:2464042/69‑1 (MQ=255)
tAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCa < 1:2366809/67‑1 (MQ=255)
ttcggtttcggGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCAGATg < 1:631178/67‑1 (MQ=255)
|
CAGGCTGCCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGCCAGATG > W3110S.gb/3815848‑3815980
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
