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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,333,478 |
G→A |
17.0% |
R555H (CGC→CAC) |
yjdA → |
conserved hypothetical protein with nucleoside triphosphate hydrolase domain |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,333,478 | 0 | G | A | 17.0%
| 132.2
/ 18.3
| 53 | R555H (CGC→CAC) | yjdA | conserved hypothetical protein with nucleoside triphosphate hydrolase domain |
| Reads supporting (aligned to +/- strand): ref base G (19/25); new base A (5/4); total (24/29) |
| Fisher's exact test for biased strand distribution p-value = 7.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.35e-01 |
AGTCGCGACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCATTT > W3110S.gb/4333408‑4333541
|
aGTCGCGACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCg > 1:2300275/1‑71 (MQ=255)
gcgACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGccc < 1:2130448/70‑1 (MQ=255)
cTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCAtt > 1:2763569/1‑70 (MQ=255)
cTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCAtt > 1:1888966/1‑70 (MQ=255)
tACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAg > 1:4644549/1‑70 (MQ=255)
tACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAg < 1:1250859/70‑1 (MQ=255)
cGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGca < 1:2390878/70‑1 (MQ=255)
cGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGca < 1:1438039/70‑1 (MQ=255)
tGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCAccc < 1:4340466/58‑1 (MQ=255)
tGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCAccc < 1:1313358/58‑1 (MQ=255)
cGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGt > 1:1032994/1‑71 (MQ=255)
ttttGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTc > 1:2168450/1‑70 (MQ=255)
ttttGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTCa < 1:1710817/71‑1 (MQ=255)
tttGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCa > 1:1613061/1‑70 (MQ=255)
ttGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTCaa < 1:4848692/70‑1 (MQ=255)
gCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCaaaa < 1:4299209/70‑1 (MQ=255)
ccGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGcaac < 1:1847624/60‑1 (MQ=255)
gAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGcaacaa > 1:1557411/1‑60 (MQ=255)
tGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATgg > 1:331129/1‑65 (MQ=255)
aaTCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGc < 1:2783726/71‑1 (MQ=255)
cACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGaa > 1:4902506/1‑61 (MQ=255)
cACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAg < 1:3888496/70‑1 (MQ=255)
tttGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAgg > 1:4443970/1‑70 (MQ=255)
tGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTc > 1:1925575/1‑65 (MQ=255)
tGCCGGGTGTTAACCGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTc > 1:3409827/1‑65 (MQ=255)
gCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGtt > 1:4475358/1‑70 (MQ=255)
gCCGGGTGTTAACCGATGTTATTCGCCCCATTGAG‑AACAAGTCAAAATGGAATTGAGCGAg > 1:3776013/1‑61 (MQ=255)
gCCGGGTGTTAACCGATGTTATTCGACCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGttt > 1:4113655/1‑71 (MQ=255)
ccGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGtt < 1:1910932/69‑1 (MQ=255)
tgtTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGa > 1:2594353/1‑55 (MQ=255)
tgtTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCt < 1:4729941/71‑1 (MQ=255)
ttAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGa < 1:4666803/44‑1 (MQ=255)
ttAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGc < 1:3843451/51‑1 (MQ=255)
aaCCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGt > 1:1956084/1‑71 (MQ=255)
aaCCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGt > 1:736940/1‑71 (MQ=255)
aCCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGtt < 1:2153063/71‑1 (MQ=255)
ccGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATgg < 1:2163082/39‑1 (MQ=255)
cGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTc < 1:1256809/71‑1 (MQ=255)
cGATGTTATTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGttt > 1:3262442/1‑70 (MQ=255)
gATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGaa > 1:1278510/1‑39 (MQ=255)
gATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCg < 1:4968785/59‑1 (MQ=255)
aTGTTATTCGCCCCATTGAGCAACAAGTCAAAATg < 1:3865567/35‑1 (MQ=255)
tGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAggg > 1:5054240/1‑52 (MQ=255)
tGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAggg > 1:933769/1‑52 (MQ=255)
tGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCAtt < 1:1435116/71‑1 (MQ=255)
tGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTATCGTcc < 1:11298/60‑1 (MQ=255)
gTTATTCGCCCCATTGAGCAACAAGTCAAAATGGa > 1:5111823/1‑35 (MQ=255)
ttATTCGCCCCATTGAGCAACAAGTCAAAATGGaa < 1:3590165/35‑1 (MQ=255)
ttATTCGCCCCATTGAGCAACAAGTCAAAATGGaa < 1:3191043/35‑1 (MQ=255)
ttATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCa < 1:4732805/67‑1 (MQ=255)
ttATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCa < 1:3262913/67‑1 (MQ=255)
ttATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCAttt < 1:3930402/70‑1 (MQ=255)
ttATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCAttt < 1:3409759/70‑1 (MQ=255)
aTTCACCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCt > 1:424986/1‑57 (MQ=255)
|
AGTCGCGACTTTACGCTGCGTTTTGCCGAGCTTGAATCCACCCTTTGCCGGGTGTTAACCGATGTTATTCGCCCCATTGAGCAACAAGTCAAAATGGAATTGAGCGAGTCAGGGTTTCGTCCTGGGTTTCATTT > W3110S.gb/4333408‑4333541
|
| 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
