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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
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 | 98.1%
| 175.9
/ ‑4.5
| 53 | V130A (GTA→GCA) | ycdT | predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (25/27); minor base G (1/0); total (26/27) |
| Fisher's exact test for biased strand distribution p-value = 4.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-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. |
GTCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTTG > W3110S.gb/1093619‑1093750
|
gtCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAt < 1:116524/70‑1 (MQ=255)
tCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTg < 1:4407875/71‑1 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt > 1:4339955/1‑71 (MQ=255)
aTGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAAt < 1:1523834/71‑1 (MQ=255)
tGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAAt > 1:2549892/1‑70 (MQ=255)
aTTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt < 1:4601475/71‑1 (MQ=255)
ttGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt < 1:3689056/61‑1 (MQ=255)
tGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt > 1:3638681/1‑69 (MQ=255)
cAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATa < 1:314457/63‑1 (MQ=255)
tCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAt < 1:513793/51‑1 (MQ=255)
tCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGa > 1:3764622/1‑70 (MQ=255)
tattatTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt > 1:2339493/1‑53 (MQ=255)
tattatTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:1306780/1‑71 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaa < 1:1696195/68‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:847321/67‑1 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac < 1:2541861/70‑1 (MQ=255)
attTGTTTCGTCAGATGAGTTTGTGCATATTAATTTTTCTGGCATTg < 1:3572279/47‑1 (MQ=39)
attTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGt > 1:3852549/1‑58 (MQ=255)
attTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAacac < 1:3003305/70‑1 (MQ=255)
tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAg > 1:4188294/1‑60 (MQ=255)
tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATT‑GTGAATAAAGTTAGTGAAAACACaa < 1:3525125/70‑1 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa > 1:2135016/1‑71 (MQ=255)
gTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa < 1:4020141/70‑1 (MQ=255)
gTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa < 1:3477996/70‑1 (MQ=255)
tttCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACa < 1:957090/71‑1 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGt > 1:1375121/1‑53 (MQ=255)
tCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa < 1:3015482/57‑1 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:1324241/1‑55 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAat > 1:3040917/1‑71 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAat > 1:1530458/1‑71 (MQ=255)
gATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaaa < 1:2222134/43‑1 (MQ=255)
gATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatt > 1:725424/1‑71 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGt > 1:352643/1‑48 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGt > 1:561966/1‑48 (MQ=255)
gAGTTTGTGCATATTAATATTTCTGGCATTGGTGaa > 1:11285/1‑36 (MQ=255)
aGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttat < 1:4043144/70‑1 (MQ=255)
tttGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt < 1:515050/66‑1 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttat > 1:1309709/1‑66 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTc < 1:3771172/70‑1 (MQ=255)
gtgCATATTAATATTTCTGGCATTGGTGAATAAAGt < 1:1770770/36‑1 (MQ=255)
cATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaa > 1:4067273/1‑70 (MQ=255)
tatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaaa < 1:1743274/71‑1 (MQ=255)
atTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaaaa > 1:2094690/1‑71 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACa > 1:620147/1‑47 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACa > 1:614728/1‑47 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTcc < 1:3470366/63‑1 (MQ=255)
tAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa > 1:37782/1‑67 (MQ=255)
aaTATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATg < 1:3039354/70‑1 (MQ=255)
tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa < 1:2793995/41‑1 (MQ=255)
tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACt > 1:971042/1‑71 (MQ=255)
tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACttt < 1:1487509/71‑1 (MQ=255)
ttCTGGGATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTtg > 1:4445436/1‑71 (MQ=255)
ttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTtg > 1:1711690/1‑71 (MQ=255)
|
GTCCAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTTG > W3110S.gb/1093619‑1093750
|
| 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
