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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
656,044 |
T→C |
18.4% |
F44L (TTC→CTC) |
ycbS → |
predicted outer membrane usher protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 656,044 | 0 | T | C | 18.4%
| 172.8
/ 34.5
| 76 | F44L (TTC→CTC) | ycbS | predicted outer membrane usher protein |
| Reads supporting (aligned to +/- strand): ref base T (27/35); new base C (7/7); total (34/42) |
| Fisher's exact test for biased strand distribution p-value = 7.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.07e-01 |
GGCTGGTGGTGTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGCCAGG > minE/655979‑656111
|
ggCTGGTGGTGTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCaa < 1:2890803/70‑1 (MQ=255)
gtggtgTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTTGATCCTGCTTTTTTCAAAga < 1:1049636/68‑1 (MQ=255)
gtggtgTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAga < 1:3175248/68‑1 (MQ=255)
gtggtgTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAga < 1:3803067/68‑1 (MQ=255)
gtggtgTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACATGGTTCGATCCTGCTTTTTTCAAAga < 1:2977535/68‑1 (MQ=255)
ttGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTtctc > 1:1487798/1‑56 (MQ=255)
ttGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTCTCa > 1:3745713/1‑57 (MQ=255)
ttGTGTCGGCAGCGTTCAATGAACAAGCTGAAACCTGGTTCGATCCTGCTTTTCTCa > 1:670521/1‑57 (MQ=39)
tgtgTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCaa > 1:3595086/1‑71 (MQ=255)
tgtgTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTCTCAAAGATGATCCCTCaa > 1:3872112/1‑71 (MQ=255)
gtgtCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTCTCAAAGATGATCCCTCaa < 1:2609267/70‑1 (MQ=255)
gCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCaa < 1:3483707/50‑1 (MQ=255)
gCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCaa < 1:2193596/50‑1 (MQ=255)
gCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCaa < 1:1974703/50‑1 (MQ=255)
cGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGAt < 1:3363834/71‑1 (MQ=255)
cGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGAt < 1:3821941/71‑1 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTg > 1:3369707/1‑70 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTg > 1:277150/1‑70 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTg > 1:147340/1‑70 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTg > 1:1111867/1‑70 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGt > 1:3216162/1‑71 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGt > 1:3157311/1‑71 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGt > 1:532023/1‑71 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGt > 1:760928/1‑71 (MQ=255)
cAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGT‑‑CCGATTTGtc > 1:1393375/1‑70 (MQ=255)
aaTGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGt < 1:3682366/70‑1 (MQ=255)
aaTGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGt < 1:2395602/70‑1 (MQ=255)
aaTGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGtc > 1:527349/1‑71 (MQ=255)
gCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCg > 1:956737/1‑71 (MQ=255)
gCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCg > 1:315458/1‑71 (MQ=255)
cacaAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGt > 1:542232/1‑71 (MQ=255)
aaGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGcc < 1:1046363/56‑1 (MQ=255)
aaGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGcc < 1:2890797/56‑1 (MQ=255)
aaGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGcc < 1:2410567/56‑1 (MQ=255)
aaGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGcc < 1:3736224/56‑1 (MQ=255)
aGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAAt < 1:1257035/48‑1 (MQ=255)
aGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAAt < 1:649418/48‑1 (MQ=255)
aGCTGAAACCTGGTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTc > 1:2362800/1‑70 (MQ=255)
aGCTGAAACCTGGTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTc > 1:1776685/1‑70 (MQ=255)
cTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAAtgg > 1:3995252/1‑48 (MQ=255)
cTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAAtgg > 1:3482826/1‑48 (MQ=255)
aaCCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAg < 1:1412112/71‑1 (MQ=255)
aaCCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAg < 1:2711978/71‑1 (MQ=255)
aaCCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAg < 1:2643769/71‑1 (MQ=255)
aaCCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAg < 1:244397/71‑1 (MQ=255)
gTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACaaa < 1:3406802/71‑1 (MQ=255)
gTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACaaa < 1:144427/71‑1 (MQ=255)
gTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACaa > 1:1037410/1‑70 (MQ=255)
gTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACaa > 1:2169629/1‑70 (MQ=255)
tCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACaaaa > 1:1700560/1‑70 (MQ=255)
gATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:1258585/71‑1 (MQ=255)
gATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:3380203/71‑1 (MQ=255)
gATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:3968915/71‑1 (MQ=255)
gATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:1094825/71‑1 (MQ=255)
gATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:650257/71‑1 (MQ=255)
gATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:1444422/71‑1 (MQ=255)
gATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:3993358/71‑1 (MQ=255)
aTCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAAt < 1:3262356/70‑1 (MQ=255)
aTCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:2372477/57‑1 (MQ=255)
aTCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:2812611/57‑1 (MQ=255)
aTCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:3252275/57‑1 (MQ=255)
aTCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:1527848/57‑1 (MQ=255)
tCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATaa > 1:3045215/1‑71 (MQ=255)
cTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:371054/54‑1 (MQ=255)
cTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:755216/54‑1 (MQ=255)
cTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:2787805/54‑1 (MQ=255)
cTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:1161496/54‑1 (MQ=255)
cTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGaaa < 1:3837653/54‑1 (MQ=255)
tGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGttt > 1:3496537/1‑48 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:1009676/1‑70 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:970320/1‑70 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:1292138/1‑70 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:1570606/1‑70 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:2345721/1‑70 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:2857762/1‑70 (MQ=255)
gCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:3019517/1‑70 (MQ=255)
gCTTTTTACAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGc > 1:2839214/1‑70 (MQ=255)
tttctCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGCCAgg > 1:1345417/1‑71 (MQ=255)
tttctCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGCCAgg > 1:1550758/1‑71 (MQ=255)
|
GGCTGGTGGTGTTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACAAAAAATAACGCCAGG > minE/655979‑656111
|
| 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
