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 |
1,231,014 |
C→T |
23.1% |
G581D (GGT→GAT) |
ptrB ← |
protease II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,231,014 | 0 | C | T | 23.1%
| 77.2
/ 19.6
| 39 | G581D (GGT→GAT) | ptrB | protease II |
| Reads supporting (aligned to +/- strand): ref base C (14/16); new base T (5/4); total (19/20) |
| Fisher's exact test for biased strand distribution p-value = 7.16e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.82e-01 |
GTGCGGTGACGTTGTCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCATCGTTGTTACAACATCAACAA > minE/1230946‑1231083
|
gtgCGGTGACGTTGTCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGAGGGTTAccc > 1:216265/1‑71 (MQ=255)
tgCGGTGACGTTGTCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTAtcc < 1:1096005/70‑1 (MQ=255)
tGTCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTATCCCACTCTTCAAAc > 1:1124559/1‑71 (MQ=255)
tCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTATCCCACTCTTCAAACt > 1:895343/1‑70 (MQ=255)
tCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACt < 1:1101868/70‑1 (MQ=255)
tACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCAcc < 1:307151/71‑1 (MQ=255)
tACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCAc < 1:2015606/70‑1 (MQ=255)
cGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCAc > 1:1607234/1‑68 (MQ=255)
cTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCa < 1:1838970/50‑1 (MQ=255)
aGCTTTACATGTACTCGTAATATTGCGGATCCTGCGGGTTATCCCACTCTTCAAACTCACCa > 1:211/1‑62 (MQ=255)
gCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAagag > 1:395764/1‑71 (MQ=255)
cTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAgg < 1:1620820/71‑1 (MQ=255)
cTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAgg < 1:470027/71‑1 (MQ=255)
cATGTACTCGTAATATTGCGGATCCTGCGGGTTAcc > 1:1406806/1‑36 (MQ=255)
cATGTACTCGTAATATTGCGGATCCTGCGGGTTATCCCACTCTTCAAACTCACCAGTGGTAag > 1:2068260/1‑63 (MQ=255)
cATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAAtt < 1:768901/70‑1 (MQ=255)
tGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGAt < 1:1251565/71‑1 (MQ=255)
gTAGTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGa > 1:2085587/1‑69 (MQ=255)
gTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGa > 1:1078984/1‑69 (MQ=255)
gTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGa > 1:555863/1‑69 (MQ=255)
tCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAgg < 1:850087/59‑1 (MQ=255)
cGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGa < 1:874524/64‑1 (MQ=255)
cGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtc > 1:6592/1‑67 (MQ=255)
cGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtc > 1:9296/1‑67 (MQ=255)
cGTAATATTGCGGATCCTGCGGGTTACCCAACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtc > 1:675760/1‑67 (MQ=255)
gTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtcatc < 1:12718/69‑1 (MQ=255)
gTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtcatc < 1:244638/69‑1 (MQ=255)
gTAATAATGCGGATCCTGCGGGTTATCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtcatc > 1:1883649/1‑69 (MQ=255)
tAATATTGCGGATCCTGCGGGTTATCCCACTCTTCAAACTCAc < 1:960574/43‑1 (MQ=255)
atatTGCGGATCCTGCGGGTTATCCCACTCTTCAAACTCACCAGTGGTa < 1:2068749/49‑1 (MQ=255)
atatTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCa > 1:1963603/1‑71 (MQ=255)
tatTGCGGATCCTGCGGGTTATCCCACTCTTCAAACTCACCAGTGGTAAGATGa < 1:1160682/54‑1 (MQ=39)
tatTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGAtt < 1:1993635/61‑1 (MQ=255)
ttGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGaa > 1:958584/1‑53 (MQ=255)
gCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTaa > 1:1617711/1‑45 (MQ=255)
gCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTaa > 1:1257220/1‑45 (MQ=255)
gggATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTaa > 1:337438/2‑44 (MQ=255)
gATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtca < 1:959947/56‑1 (MQ=255)
tCCTGAGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCATCGTTGTTac < 1:1599834/71‑1 (MQ=255)
gCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATtcatc > 1:1356792/1‑52 (MQ=255)
ggTTATCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCATCGTTGTTACAACATca < 1:572301/71‑1 (MQ=255)
ggTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCAt < 1:1143935/55‑1 (MQ=255)
ccccACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCATCGTTGTTACAACATcaacaa < 1:516962/70‑1 (MQ=255)
ccccACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCATCGTTGTTACAACATcaacaa < 1:1411291/70‑1 (MQ=255)
|
GTGCGGTGACGTTGTCATACGGGCTGTAGCTTTTCATGTACTCGTAATATTGCGGATCCTGCGGGTTACCCCACTCTTCAAACTCACCAGTGGTAAGAGGAATTGATTCATCAAGCATCGTTGTTACAACATCAACAA > minE/1230946‑1231083
|
| 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
