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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,474,830 |
T→A |
16.2% |
intergenic (+128/‑106) |
nrdA → / → nrdB |
ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,474,830 | 0 | T | A | 16.2%
| 82.7
/ 10.9
| 37 | intergenic (+128/‑106) | nrdA/nrdB | ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
| Reads supporting (aligned to +/- strand): ref base T (14/17); new base A (3/3); total (17/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 |
CCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTAAAATG > minE/1474761‑1474899
|
ccTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTa < 1:1978563/71‑1 (MQ=255)
gATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑g > 1:1061637/1‑70 (MQ=255)
tAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCt > 1:1044833/1‑71 (MQ=255)
tAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCt > 1:619846/1‑71 (MQ=255)
aGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCg < 1:3726169/71‑1 (MQ=255)
gTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGcc > 1:3649567/1‑71 (MQ=255)
cATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGAt < 1:563601/71‑1 (MQ=255)
cATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGAt < 1:1550958/71‑1 (MQ=255)
tCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGAt > 1:1891044/1‑69 (MQ=255)
aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAg < 1:278203/70‑1 (MQ=255)
ggCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGAc > 1:549119/1‑71 (MQ=255)
cTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGAcgc < 1:1673135/71‑1 (MQ=255)
gTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATa < 1:844341/59‑1 (MQ=255)
gTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGc > 1:139728/1‑71 (MQ=255)
gTGCCGGATGCAGCGTGAACGCATTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGc > 1:1755111/1‑71 (MQ=255)
ggATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCg > 1:2861943/1‑70 (MQ=255)
gATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa < 1:2643893/71‑1 (MQ=255)
gATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa > 1:3642708/1‑71 (MQ=255)
aTGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCAt < 1:1398706/71‑1 (MQ=255)
aGCGTAAACGCCTGATCCGTCCAAC‑‑‑‑GGTTCG‑G‑‑ATTTTGTAGGCCTGATAAGAcgcg > 1:3524888/1‑56 (MQ=2)
aGCGTAAACGCCTGATCCGTCCAAC‑‑‑‑GGTTCG‑G‑‑ATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAg > 1:3457726/1‑71 (MQ=2)
gCGTGAACGCCTTATCCGGCCTACGGATGGCGCG‑GGAA‑TTTGTAGGCCTGATAAGACGCGTTAGCGTCGCa < 1:2546502/71‑1 (MQ=0)
cGTGAACGCCTTATCCGGCCTACGGGTGGCGCGAGA‑A‑TTTGTAGGCCTGATAAGACGCGTTAGCGTCGCAt > 1:3206446/1‑71 (MQ=0)
taaaCGCCTGATCCGTCCAAC‑‑‑‑GGTTCG‑G‑‑ATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGcat < 1:3519389/69‑2 (MQ=2)
aaCGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAgg < 1:1702689/71‑1 (MQ=255)
aaCGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAg < 1:2833867/70‑1 (MQ=255)
aaCGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAg < 1:3225702/70‑1 (MQ=255)
aaCGCCTGATCCGTCCAAC‑‑‑‑GGTTCG‑G‑‑ATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGcatct < 1:1790819/71‑4 (MQ=2)
aaCGCCTGATCCGTCCAAC‑‑‑‑GGTTCG‑G‑‑ATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGcatc < 1:3415668/70‑3 (MQ=2)
aCGCCTGATCCGTCCAAC‑‑‑‑GGTTCG‑G‑‑ATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCAt > 1:2284845/1‑61 (MQ=2)
gCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATg < 1:2401244/71‑1 (MQ=255)
gCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATg < 1:3217889/71‑1 (MQ=255)
tATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggc > 1:3370307/1‑71 (MQ=255)
tATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggc > 1:1032332/1‑71 (MQ=255)
gCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATg < 1:2240725/61‑1 (MQ=255)
ccTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTAAAAt > 1:237384/1‑71 (MQ=255)
cTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTAAAATg < 1:2909558/71‑1 (MQ=255)
tAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTaa < 1:1571474/66‑1 (MQ=255)
|
CCTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAC‑‑‑‑GGCTCG‑G‑‑A‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGCGTAAAATG > minE/1474761‑1474899
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
