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 |
2,280,720 |
G→A |
30.3% |
R201* (CGA→TGA) |
fabR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,280,720 | 0 | G | A | 30.3%
| 76.2
/ 40.2
| 56 | R201* (CGA→TGA) | fabR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base G (16/23); new base A (12/5); total (28/28) |
| Fisher's exact test for biased strand distribution p-value = 7.97e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01 |
TTTTCTCTTGTTCACGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTGAAGACAA > minE/2280651‑2280785
|
ttttCTCTTGTTCACGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGc > 1:2444611/1‑71 (MQ=255)
ttGTTCACGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCtctt < 1:2846813/68‑1 (MQ=255)
ttGTTCACAGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCActc < 1:2666389/66‑1 (MQ=255)
gTTCACGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTaa < 1:1220403/70‑1 (MQ=255)
aCGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGcc < 1:1189981/71‑1 (MQ=255)
cGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCg < 1:1355680/71‑1 (MQ=255)
gCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGAc < 1:404785/71‑1 (MQ=255)
taTACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGAAGTACCAGTCGCTCTTCTAATTGCCg > 1:2736721/2‑67 (MQ=255)
gATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGAc > 1:3725502/1‑69 (MQ=255)
gATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGAc > 1:3720841/1‑69 (MQ=255)
tACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCg > 1:1352363/1‑50 (MQ=255)
tACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACgttg < 1:2548491/71‑1 (MQ=255)
ccAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACgttgtt < 1:2707388/71‑1 (MQ=255)
ccAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACgttgt < 1:1222453/70‑1 (MQ=255)
cAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGctct < 1:1086789/51‑1 (MQ=255)
aGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTc > 1:488729/1‑70 (MQ=255)
aGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCg < 1:206130/71‑1 (MQ=255)
gTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGa > 1:2491908/1‑71 (MQ=255)
gTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGa > 1:3044293/1‑71 (MQ=255)
gTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGa > 1:2704167/1‑71 (MQ=255)
taataaGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTaa < 1:3024591/53‑1 (MQ=255)
taataaGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACgttgt < 1:950147/66‑1 (MQ=255)
taataaGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGAc > 1:3231283/1‑71 (MQ=255)
ataaGCCCCTTTCGAAATAATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTc > 1:3129101/1‑66 (MQ=255)
ataaGCCCCTTTCGAAATAATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTc > 1:3133500/1‑66 (MQ=255)
aGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGa > 1:455231/1‑71 (MQ=255)
cccTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGctc > 1:2172672/1‑39 (MQ=255)
cccTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAAtt < 1:1465118/47‑1 (MQ=255)
cccTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGt < 1:660469/71‑1 (MQ=255)
gAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGc > 1:196289/1‑71 (MQ=255)
aaaTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGT‑CAACGCCt < 1:2758353/71‑1 (MQ=255)
aaTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCg > 1:3824618/1‑52 (MQ=255)
aaTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCt < 1:2859376/71‑1 (MQ=255)
aaTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCt < 1:3838214/71‑1 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCt < 1:3745131/70‑1 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCt < 1:568202/70‑1 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTc > 1:638567/1‑71 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTc > 1:3826911/1‑71 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCGCTATTCTAATTGCCGACGTTGTTCGACGCCg > 1:3131689/1‑57 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTc > 1:3864641/1‑71 (MQ=255)
aTCATTCGCAGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTc > 1:1265024/1‑71 (MQ=255)
tCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCg < 1:368088/71‑1 (MQ=255)
tCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTGGACGTCGGCg > 1:69428/1‑55 (MQ=255)
aGTTGCAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGa > 1:776582/1‑43 (MQ=255)
gTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCa < 1:1080157/71‑1 (MQ=255)
gTTGCAGTACCAGGCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCa < 1:3453145/71‑1 (MQ=255)
ttGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCAc > 1:1303221/1‑71 (MQ=255)
cAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTg < 1:3805537/70‑1 (MQ=255)
cAGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTg < 1:3412211/70‑1 (MQ=255)
aGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCg > 1:995572/1‑36 (MQ=255)
aGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCg > 1:3864287/1‑36 (MQ=255)
aGTACCAGTCACTCTTCTAATTGCCGACGTTGTTCg > 1:3110414/1‑36 (MQ=255)
ccAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTGAAGAc > 1:136029/1‑70 (MQ=255)
cAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAAc < 1:3414459/46‑1 (MQ=255)
cAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTc < 1:2431194/51‑1 (MQ=255)
cAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTGAAGACaa > 1:372488/1‑71 (MQ=255)
cAGTCACTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTGAAGACaa < 1:1036203/71‑1 (MQ=255)
|
TTTTCTCTTGTTCACGGCGATACCAGTAATAAGCCCCTTTCGAAATCATTCGCAGTTGCAGTACCAGTCGCTCTTCTAATTGCCGACGTTGTTCGACGCCGACGTCCAACGCCTCGGCACCCGCACTGAAGACAA > minE/2280651‑2280785
|
| 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
