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 |
2,099,387 |
T→C |
23.3% |
intergenic (+25/+71) |
hisI → / ← cld |
fused phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,099,387 | 0 | T | C | 23.3%
| 53.0
/ 15.1
| 30 | intergenic (+25/+71) | hisI/cld | fused phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains |
| Reads supporting (aligned to +/- strand): ref base T (7/16); new base C (3/4); total (10/20) |
| Fisher's exact test for biased strand distribution p-value = 6.57e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATTTAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAA > W3110S.gb/2099318‑2099448
|
gATTTAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGatat < 1:3021996/70‑1 (MQ=255)
gATTTAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGatat > 1:3291105/1‑70 (MQ=255)
gATTTAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATAtt > 1:3744326/1‑71 (MQ=255)
gATTTAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATAtt > 1:856803/1‑71 (MQ=255)
tttAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATAttgt < 1:1216663/71‑1 (MQ=255)
tAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATAttgttg > 1:4772549/1‑71 (MQ=255)
tAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATAttgttg > 1:4178111/1‑71 (MQ=255)
tAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATAttgtt < 1:218491/70‑1 (MQ=255)
ggTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGatat > 1:933294/1‑59 (MQ=255)
ggTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGatat > 1:4612544/1‑59 (MQ=255)
gTATTTGAGTACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATcc < 1:2553648/71‑1 (MQ=255)
gTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATcc < 1:2876039/71‑1 (MQ=255)
gTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATcc < 1:2886129/71‑1 (MQ=255)
ttGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCa < 1:3518067/71‑1 (MQ=255)
aaCCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCaaaaaa < 1:2360437/71‑1 (MQ=255)
aCCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCaaaaaaa < 1:2169228/71‑1 (MQ=255)
ccTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAAc < 1:4202998/71‑1 (MQ=255)
ccTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAAc < 1:1364849/71‑1 (MQ=255)
cTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGatat < 1:812770/46‑1 (MQ=255)
cTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGatat < 1:4811064/46‑1 (MQ=255)
tGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATcc < 1:3959197/58‑1 (MQ=255)
gCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCaaaaaaa > 1:2217438/1‑67 (MQ=255)
cGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGc < 1:1095618/71‑1 (MQ=255)
tAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCaaaaaaa < 1:2824340/64‑1 (MQ=255)
tAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCaa < 1:538630/71‑1 (MQ=255)
tAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCaa < 1:1125976/71‑1 (MQ=255)
aaCGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAg < 1:2988880/70‑1 (MQ=255)
aaCGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAg < 1:1029061/70‑1 (MQ=255)
aaCGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCAAgg < 1:3787343/71‑1 (MQ=255)
ggCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGgtgt < 1:2954004/71‑1 (MQ=255)
tCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTcac > 1:1658307/1‑70 (MQ=255)
aGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTcaccac > 1:4388765/1‑71 (MQ=255)
tGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCACCAccc > 1:2948148/1‑71 (MQ=255)
aGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGgt > 1:2364199/1‑59 (MQ=255)
gCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCACCACCCTGCCCt > 1:4197454/1‑71 (MQ=255)
tAAGCGGATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCaa < 1:4316028/46‑1 (MQ=255)
tAAGCGGATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCaa < 1:3859059/46‑1 (MQ=255)
aGCGGATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCaa > 1:4253028/1‑44 (MQ=255)
aGCGGATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCaa > 1:933511/1‑44 (MQ=255)
aGCGGATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCaccacc > 1:736317/1‑56 (MQ=255)
ggATGCGATACTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTaa < 1:3982776/70‑1 (MQ=255)
gATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTaaaa > 1:3816893/1‑71 (MQ=255)
atTGTTGCCGCATCCGGCAAAAAAACGGGCAAGgtgt < 1:5059813/37‑1 (MQ=255)
atTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTcac < 1:857344/40‑1 (MQ=255)
|
GATTTAACGACGGTAATTGAGAACCTGCGTAAACGGCATCAGTGAGTTGCGGGGTAAGCGGATGCGATATTGTTGCCGCATCCGGCAAAAAAACGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAA > W3110S.gb/2099318‑2099448
|
| 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
