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 |
2,891,414 |
C→A |
54.4% |
P23P (CCC→CCA) |
ytfQ → |
predicted sugar transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,891,414 | 0 | C | A | 54.4%
| 7.1
/ 104.4
| 68 | P23P (CCC→CCA) | ytfQ | predicted sugar transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (16/15); new base A (11/26); total (27/41) |
| Fisher's exact test for biased strand distribution p-value = 8.43e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-01 |
TGTGGAAACGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAATGTGGCGAA > minE/2891347‑2891482
|
tgtgGAAACGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTa < 1:418485/71‑1 (MQ=255)
tgGAAACGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAAc > 1:1820166/1‑71 (MQ=255)
tgGAAACGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTaa < 1:3356470/70‑1 (MQ=255)
aaaCGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGt < 1:2685221/71‑1 (MQ=255)
aCGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTg > 1:1132957/1‑71 (MQ=255)
aCGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTg > 1:318315/1‑71 (MQ=255)
cGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTgg < 1:42492/71‑1 (MQ=255)
cttacttaTAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGAt > 1:921369/1‑71 (MQ=255)
acttaTAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGAttt < 1:3908750/70‑1 (MQ=255)
cttaTAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGAtttt < 1:2596769/70‑1 (MQ=255)
ataGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCg > 1:2861598/1‑69 (MQ=255)
ataGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGc < 1:3351605/70‑1 (MQ=255)
ataGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTa < 1:2161674/54‑1 (MQ=255)
ataGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTa < 1:541637/54‑1 (MQ=255)
ataGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGc < 1:1856166/70‑1 (MQ=255)
aGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAg > 1:3408748/1‑70 (MQ=255)
ctctGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGtcg > 1:489079/1‑71 (MQ=255)
tGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcgg < 1:258396/69‑1 (MQ=255)
cAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGt > 1:681048/1‑49 (MQ=255)
cAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGt > 1:1968536/1‑49 (MQ=255)
cAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGt < 1:2010274/49‑1 (MQ=255)
cAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGtcgga < 1:3089157/68‑1 (MQ=255)
cAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGtcgga < 1:499906/68‑1 (MQ=255)
aGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGtcggatcg > 1:871396/1‑70 (MQ=255)
gTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcggatcgga < 1:885768/71‑1 (MQ=255)
gTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcggatcgg > 1:3676678/1‑70 (MQ=255)
tctcGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGAttt < 1:3723029/53‑1 (MQ=255)
tctcGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCg < 1:1939772/56‑1 (MQ=255)
ctcGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcg > 1:3271615/1‑62 (MQ=255)
ctcGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcg > 1:2850521/1‑62 (MQ=255)
ctcGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGaa > 1:3886563/1‑70 (MQ=255)
tcGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAAt > 1:3601053/1‑70 (MQ=255)
ggCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAg > 1:1839604/1‑71 (MQ=255)
ggCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCTTTGGATTTTCGCAGGTCGGATCGGAATc < 1:2108057/69‑1 (MQ=255)
gCAGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGtcggat < 1:847958/61‑1 (MQ=255)
aGCCATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATc > 1:3640409/1‑66 (MQ=255)
gCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTg < 1:1303564/71‑1 (MQ=255)
ccATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTg > 1:1888078/1‑70 (MQ=255)
cATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGc < 1:1183195/71‑1 (MQ=255)
cATGTCGTCTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGc < 1:3402175/71‑1 (MQ=255)
tGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcgga < 1:132197/53‑1 (MQ=255)
tGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGt > 1:13267/1‑71 (MQ=255)
tcgtcTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTgg < 1:1854533/66‑1 (MQ=255)
tcgtcTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTg < 1:1544429/70‑1 (MQ=255)
tcgtcTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTg < 1:1181534/70‑1 (MQ=255)
gtcTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGcc < 1:1984656/70‑1 (MQ=255)
gtcTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCg > 1:2338416/1‑71 (MQ=255)
cTATGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCg > 1:1267879/1‑69 (MQ=255)
aTGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGtcgg < 1:3252524/44‑1 (MQ=255)
tGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCa < 1:211090/68‑1 (MQ=255)
tGGCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGa < 1:3349980/70‑1 (MQ=255)
gCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGGTGGCGTGCCGCAGAAAc > 1:3851037/1‑71 (MQ=255)
gCGTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAAc < 1:1963135/71‑1 (MQ=255)
gTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAg < 1:860430/50‑1 (MQ=255)
gTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAg < 1:2538235/50‑1 (MQ=255)
gTTGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCa < 1:3943506/71‑1 (MQ=255)
ttGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcggatcgg < 1:1870511/43‑1 (MQ=255)
ttGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGtcggatcgg < 1:487340/43‑1 (MQ=255)
ttGGCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCa < 1:3687504/70‑1 (MQ=255)
ggCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAAt < 1:3226840/70‑1 (MQ=255)
ggCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAAt > 1:2877894/1‑44 (MQ=255)
gCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGc > 1:138553/1‑52 (MQ=255)
gCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAAtgt < 1:1587719/71‑1 (MQ=255)
gCCGCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAAtg < 1:1523635/70‑1 (MQ=255)
ccGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAAtgtg < 1:2061651/71‑1 (MQ=255)
gCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAATGTGGc > 1:1826718/1‑71 (MQ=255)
gCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAATGTGGc > 1:2996377/1‑71 (MQ=255)
gCTCCATTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAATGTGGc > 1:1977426/1‑71 (MQ=255)
ccTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAATGTGGCGaa < 1:3297028/70‑1 (MQ=255)
|
TGTGGAAACGCTTACTTATAGTCTCTGCAGTCTCGGCAGCCATGTCGTCTATGGCGTTGGCCGCTCCCTTAACCGTTGGATTTTCGCAGGTCGGATCGGAATCAGGCTGGCGTGCCGCAGAAACCAATGTGGCGAA > minE/2891347‑2891482
|
| 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
