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 |
|
A5 F1 I0 R2
|
201 |
99.6 |
7939938 |
96.9% |
7693799 |
60.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,093,686 |
T→C |
100% |
V130A (GTA→GCA) |
ycdT → |
predicted diguanylate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,093,686 | 0 | T | C | 98.3%
| 194.5
/ ‑4.9
| 58 | V130A (GTA→GCA) | ycdT | predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (22/35); minor base A (0/1); total (22/36) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTTGTG > W3110S.gb/1093620‑1093752
|
tCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTg < 1:2279002/71‑1 (MQ=255)
gACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTg < 1:637812/63‑1 (MQ=255)
aaaTTTCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa < 1:4710457/68‑1 (MQ=255)
aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa < 1:3250611/70‑1 (MQ=255)
cATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAg < 1:3027538/71‑1 (MQ=255)
ttGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGtt < 1:6998556/71‑1 (MQ=255)
gCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAg > 1:1482259/1‑71 (MQ=255)
aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGa < 1:6740082/71‑1 (MQ=255)
aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGa < 1:682528/71‑1 (MQ=255)
tCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGa > 1:6166955/1‑70 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGtt > 1:7222829/1‑61 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:6319778/67‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAaca > 1:2108538/1‑71 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAaca < 1:6172730/71‑1 (MQ=255)
attTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt < 1:1588293/58‑1 (MQ=255)
attTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt < 1:1579130/58‑1 (MQ=255)
tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:920104/71‑1 (MQ=255)
ttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa > 1:5917849/1‑70 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATa > 1:2052439/1‑51 (MQ=255)
gTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa < 1:2482964/70‑1 (MQ=255)
tCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAgc > 1:438388/1‑71 (MQ=255)
cGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa > 1:353878/1‑66 (MQ=255)
cGTCAGATGAGTTTGTGCATATTAATATTTCTGGAATTGGTGAATAAAGTTAGTGAAAACACAAAACAgc < 1:1682270/70‑1 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt < 1:6331043/37‑1 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt < 1:5497664/37‑1 (MQ=255)
tCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGtt < 1:618783/49‑1 (MQ=255)
cAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGtt < 1:7774823/48‑1 (MQ=255)
cAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt < 1:5549714/47‑1 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAg > 1:5341013/1‑45 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAat > 1:3966253/1‑71 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTG‑AAACACAAAACAGCGCAatt > 1:7013221/1‑71 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:1184964/1‑53 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:2266246/1‑53 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:3421671/58‑1 (MQ=255)
tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:3241128/57‑1 (MQ=255)
tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:1712067/57‑1 (MQ=255)
tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattta > 1:3991352/1‑71 (MQ=255)
tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt < 1:5034313/70‑1 (MQ=255)
aGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttatt < 1:892394/71‑1 (MQ=255)
aGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttat < 1:5811548/70‑1 (MQ=255)
gTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCaa > 1:7671216/1‑64 (MQ=255)
gTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttattt < 1:3698561/71‑1 (MQ=255)
gTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttattt < 1:6444320/71‑1 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:2551466/51‑1 (MQ=255)
gtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAacac < 1:5238762/48‑1 (MQ=255)
tgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaa > 1:7614216/1‑43 (MQ=255)
gCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaa > 1:5924880/1‑70 (MQ=255)
cATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattta < 1:6706340/61‑1 (MQ=255)
atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:5217907/1‑41 (MQ=255)
atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa < 1:186888/71‑1 (MQ=255)
atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa < 1:5977705/71‑1 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaaaa < 1:7576114/70‑1 (MQ=255)
tAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt > 1:7449845/1‑70 (MQ=255)
aaTATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATg < 1:4843600/70‑1 (MQ=255)
tCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttatt > 1:4670310/1‑51 (MQ=255)
tCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt > 1:5957380/1‑48 (MQ=255)
cTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTtgtg > 1:5740485/1‑71 (MQ=255)
cTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTtgt < 1:2923359/70‑1 (MQ=255)
|
TCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTTGTG > W3110S.gb/1093620‑1093752
|
| 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
