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 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,540,373 |
G→T |
8.1% |
D300Y (GAT→TAT) |
rfaJ → |
UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,540,373 | 0 | G | T | 8.1%
| 223.1
/ 3.2
| 73 | D300Y (GAT→TAT) | rfaJ | UDP‑D‑glucose:(galactosyl)lipopolysaccharide glucosyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (32/35); new base T (2/4); total (34/39) |
| Fisher's exact test for biased strand distribution p-value = 6.79e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.20e-01 |
AATTTATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAT > minE/2540303‑2540437
|
aaTTTATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACgag < 1:1542309/71‑1 (MQ=255)
tttATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGAt > 1:1743338/1‑71 (MQ=255)
tATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc > 1:1793322/1‑71 (MQ=255)
aTCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGc > 1:2180638/1‑70 (MQ=255)
tCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATc < 1:1200932/71‑1 (MQ=255)
cGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATc > 1:2046395/1‑70 (MQ=255)
ggTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCaa > 1:1650913/1‑71 (MQ=255)
gTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATCAat < 1:1065224/71‑1 (MQ=255)
tAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACgaga > 1:1644190/1‑58 (MQ=255)
aTACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattatt > 1:1754486/1‑70 (MQ=255)
taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAttt > 1:490746/1‑70 (MQ=255)
taAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAAttt > 1:254619/1‑70 (MQ=255)
aaaTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGGATTTaaa < 1:1865812/71‑1 (MQ=255)
aTAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaa < 1:1535846/71‑1 (MQ=255)
tAGCTTTAGAAAATTCCACCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaaa < 1:1716269/71‑1 (MQ=255)
aGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaa > 1:1220931/1‑69 (MQ=255)
aGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaa > 1:1126126/1‑69 (MQ=255)
gCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaaaa > 1:1768042/1‑68 (MQ=255)
tAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGCTGCGAAATCAat > 1:2101095/1‑49 (MQ=255)
aGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGatat < 1:981856/70‑1 (MQ=255)
gAAAATTCCCCCTGGAAAGATGACTCTCCACGATATGCGAAATc < 1:1599662/44‑1 (MQ=255)
gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata < 1:1224608/70‑1 (MQ=255)
gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata < 1:1692057/70‑1 (MQ=255)
gAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata < 1:622345/70‑1 (MQ=255)
aaaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaaa < 1:865767/71‑1 (MQ=255)
aaaTTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCa < 1:898284/43‑1 (MQ=255)
aTTCCCCCTGGAAAGATGACTCTCCACGAGATGCTAAATCAATTATTGAATTTAAAAAAAGATATAAACAt < 1:1887837/71‑1 (MQ=255)
ttCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATc > 1:907496/1‑71 (MQ=255)
ttCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATc < 1:2003367/71‑1 (MQ=255)
tCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattatt > 1:96771/1‑45 (MQ=255)
tCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattatt > 1:2031120/1‑45 (MQ=255)
tCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAattatt > 1:853110/1‑45 (MQ=255)
tCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTa < 1:2136476/52‑1 (MQ=255)
cccccTGGAAAGATCACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCt < 1:1874781/70‑1 (MQ=255)
ccccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt < 1:326074/71‑1 (MQ=255)
cccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTaaa < 1:1745742/51‑1 (MQ=255)
cccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt < 1:565148/71‑1 (MQ=255)
cccTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCtttt < 1:2080703/71‑1 (MQ=255)
tGGAAAGATGACTCTCCACGAGATGCGAAATCAat < 1:1280267/35‑1 (MQ=255)
tGGAAAGATGACTCTCCACGAGATGCGAAATCAat < 1:801088/35‑1 (MQ=255)
ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGaa > 1:18407/1‑41 (MQ=255)
ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt > 1:1361532/1‑66 (MQ=255)
ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa > 1:1259845/1‑68 (MQ=255)
ggAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTg > 1:960633/1‑71 (MQ=255)
gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTg < 1:1866024/70‑1 (MQ=255)
gAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc < 1:746978/71‑1 (MQ=255)
aaGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGAtata < 1:1253262/54‑1 (MQ=255)
aaGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCaa > 1:1133901/1‑71 (MQ=255)
aGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAg < 1:2061715/48‑1 (MQ=255)
tGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGa < 1:953186/46‑1 (MQ=255)
gACTCTCCACGATATGCGTAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTa > 1:474323/1‑60 (MQ=255)
gACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGa > 1:1367700/1‑45 (MQ=255)
gACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt < 1:719820/58‑1 (MQ=255)
gACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt < 1:1348476/58‑1 (MQ=255)
tctcCACTAGATGCGAAATCAATTATTGAATTTaaaaaa < 1:1020790/39‑1 (MQ=255)
tctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaa < 1:1407884/47‑1 (MQ=255)
tctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaa < 1:650983/47‑1 (MQ=255)
tctcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATta > 1:1760113/1‑71 (MQ=255)
tcCACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGc < 1:792237/59‑1 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt < 1:318203/53‑1 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCttt < 1:1861943/53‑1 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCt < 1:558724/51‑1 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAg > 1:1153897/1‑56 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAg > 1:1447852/1‑56 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAg > 1:1747477/1‑56 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtata > 1:1797951/1‑71 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtata > 1:1406636/1‑71 (MQ=255)
tcCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtata > 1:1521290/1‑71 (MQ=255)
ccACGATATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTatat > 1:1568589/1‑71 (MQ=255)
ccACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaa < 1:2181059/44‑1 (MQ=255)
cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGata > 1:1981406/1‑40 (MQ=255)
cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaaa > 1:1333483/1‑44 (MQ=255)
cACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATtat < 1:2162037/68‑1 (MQ=255)
aCGAGATGCGAAATCAATTATTGAATTTAAAAAAAGata < 1:1227449/39‑1 (MQ=255)
cGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATaaa > 1:217619/1‑42 (MQ=255)
|
AATTTATCCATCGGTAAAATACTATAAAATAGCTTTAGAAAATTCCCCCTGGAAAGATGACTCTCCACGAGATGCGAAATCAATTATTGAATTTAAAAAAAGATATAAACATCTTTTAGTGCAACATCATTATAT > minE/2540303‑2540437
|
| 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
