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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,628,526 |
G→T |
30.1% |
V332V (GTG→GTT) |
livJ → |
leucine/isoleucine/valine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,628,526 | 0 | G | T | 30.1%
| 63.8
/ 27.4
| 53 | V332V (GTG→GTT) | livJ | leucine/isoleucine/valine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base G (2/35); new base T (6/10); total (8/45) |
| Fisher's exact test for biased strand distribution p-value = 6.51e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.32e-01 |
CAGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTA > minE/2628461‑2628592
|
cAGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTg < 1:2800593/66‑1 (MQ=255)
aGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGAt < 1:593907/68‑1 (MQ=255)
aGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGAt < 1:3392532/68‑1 (MQ=255)
aGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGAt < 1:2491802/68‑1 (MQ=255)
aGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGAt < 1:1469901/68‑1 (MQ=255)
aGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGAt < 1:177519/68‑1 (MQ=255)
ggCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATAc < 1:683476/69‑1 (MQ=255)
ggCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATAc < 1:2158145/69‑1 (MQ=255)
ggCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATAc < 1:2026585/69‑1 (MQ=255)
gggCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGt < 1:2695261/69‑1 (MQ=255)
gggCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGt < 1:91666/69‑1 (MQ=255)
gggCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGt < 1:3356279/69‑1 (MQ=255)
gggCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGt < 1:2187145/69‑1 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:266942/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:3115631/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:3250649/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:3033380/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:2991134/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:2936418/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:3286455/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:1702533/69‑2 (MQ=255)
ggCCTGAATCAGTCTGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGtg < 1:1945972/69‑2 (MQ=255)
aaTCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATgg < 1:2110076/67‑1 (MQ=255)
cTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:718167/69‑1 (MQ=255)
cTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:1440106/69‑1 (MQ=255)
cTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:3397302/69‑1 (MQ=255)
cTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:2955784/69‑1 (MQ=255)
cTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:1583574/69‑1 (MQ=255)
tGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGTGATGGGGCCGCTGAc > 1:1332954/1‑69 (MQ=255)
tGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGTGATGGGGCCGCTGAc > 1:345662/1‑69 (MQ=255)
tGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGTGATGGGGCCGCTGAc > 1:1344134/1‑69 (MQ=255)
tGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGTGATGGGGCCGCTGAc > 1:1400855/1‑69 (MQ=255)
tGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGTGATGGGGCCGCTGAc > 1:868661/1‑69 (MQ=255)
tGACGATCCGGCGGAGATCGCTAAATACCTGAAAGCGAACTCGGTTGATACGGTGATGGGGCCGCTGAc > 1:1188045/1‑69 (MQ=255)
gaggATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTTGATACCGTAATGGGACCGCTGa < 1:3279910/64‑1 (MQ=255)
gATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCt < 1:1872837/67‑1 (MQ=255)
gATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCt < 1:2686121/67‑1 (MQ=255)
ccGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:3012547/61‑1 (MQ=255)
ccGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:597803/61‑1 (MQ=255)
aaaTCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGt < 1:1407718/40‑1 (MQ=255)
aaaTCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAg > 1:3408827/1‑69 (MQ=255)
tCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCg < 1:2678938/69‑1 (MQ=255)
tCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCg < 1:2535934/69‑1 (MQ=255)
tCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCg < 1:2295670/69‑1 (MQ=255)
tCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCg < 1:2424219/69‑1 (MQ=255)
aaGCGAACTCCGTGGATACCGTAATGGGACCGCTGa < 1:2264847/36‑1 (MQ=255)
aGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGa > 1:669536/1‑69 (MQ=255)
tCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGct < 1:3057489/46‑2 (MQ=255)
tGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:2258840/68‑1 (MQ=255)
tGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:808746/68‑1 (MQ=255)
tGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:126400/68‑1 (MQ=255)
tGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:498541/68‑1 (MQ=255)
tGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:1030716/68‑1 (MQ=255)
tGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:3331807/68‑1 (MQ=255)
ggATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTa < 1:570866/67‑1 (MQ=255)
|
CAGGCGGGCCTGAATCAGTCTGACGATCCGGCTGAAATCGCCAAATACCTGAAAGCGAACTCCGTGGATACCGTAATGGGACCGCTGACCTGGGATGAGAAAGGCGATCTGAAAGGCTTTGAGTTCGGCGTA > minE/2628461‑2628592
|
| 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
