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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
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 | 98.0%
| 161.6
/ ‑5.2
| 48 | V130A (GTA→GCA) | ycdT | predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (22/25); minor base A (1/0); total (23/25) |
| Fisher's exact test for biased strand distribution p-value = 4.79e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-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. |
GTCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACT > W3110S.gb/1093619‑1093747
|
gtCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt > 1:3038659/1‑71 (MQ=255)
gtCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt > 1:294042/1‑71 (MQ=255)
tCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTg < 1:1932325/71‑1 (MQ=255)
ccAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTgg > 1:1646163/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGAATATTAATATTTCTGGCATTGGt > 1:2998109/1‑71 (MQ=255)
cATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATT‑GTGAATAAAGt < 1:3525481/71‑1 (MQ=255)
gCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGATAg > 1:1328028/1‑71 (MQ=255)
cAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGt < 1:4122243/71‑1 (MQ=255)
tCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGa > 1:740970/1‑70 (MQ=255)
cTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAg > 1:1585488/1‑62 (MQ=255)
tattatTTGTTTCGTCAGATGAGTTTGTGTATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:288950/1‑71 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt < 1:445060/60‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:1928309/67‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:4313957/67‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:4465873/67‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAaca > 1:3919441/1‑71 (MQ=255)
tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:78162/71‑1 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa > 1:2480179/1‑71 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa > 1:3842781/1‑71 (MQ=255)
gTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTa > 1:663995/1‑56 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAg > 1:3475636/1‑52 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaa < 1:4137583/57‑1 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaa < 1:3619643/57‑1 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaa < 1:3625119/57‑1 (MQ=255)
tCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt < 1:1376561/36‑1 (MQ=255)
cAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAg > 1:1180650/1‑46 (MQ=255)
cAGATGAGTTTGTGCATATTAATATTTCTGGAATTGGTGAATAAAGTTAGTGaaaa > 1:2955142/1‑56 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:2310436/58‑1 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt < 1:2617569/71‑1 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt < 1:4561982/71‑1 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt < 1:3830083/71‑1 (MQ=255)
gAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttat > 1:195368/1‑71 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTc > 1:3547817/1‑70 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTc > 1:159892/1‑70 (MQ=255)
tatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:4482760/45‑1 (MQ=255)
tatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:1217070/45‑1 (MQ=255)
tatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGAGCAATTTATTTTCCa < 1:3802343/66‑1 (MQ=255)
atTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa < 1:3794034/39‑1 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:134109/43‑1 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaaa > 1:2692046/1‑69 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt > 1:3991442/1‑71 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt > 1:142114/1‑71 (MQ=255)
tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACt < 1:3501518/71‑1 (MQ=255)
tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaa < 1:4253802/38‑1 (MQ=255)
tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:667073/37‑1 (MQ=255)
ttCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa < 1:243261/36‑1 (MQ=255)
tGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttatt > 1:3037167/1‑49 (MQ=255)
tGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttatt > 1:4592486/1‑49 (MQ=255)
|
GTCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACT > W3110S.gb/1093619‑1093747
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
