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 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
402,650 |
C→T |
39.6% |
G38D (GGC→GAC) |
rlpA ← |
minor lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 402,650 | 0 | C | T | 39.6%
| 38.2
/ 49.1
| 48 | G38D (GGC→GAC) | rlpA | minor lipoprotein |
| Reads supporting (aligned to +/- strand): ref base C (22/7); new base T (10/9); total (32/16) |
| Fisher's exact test for biased strand distribution p-value = 1.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCTGATTTGCCGTCGCGTTCAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTACATGCCGC > minE/402585‑402717
|
ccTGATTTGCCGTCGCGTTCAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGtt > 1:1837879/1‑70 (MQ=255)
cTGATTTGCCGTCGCGTTCAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTa > 1:1895207/1‑70 (MQ=255)
aTTTGCCGTCGCGTTCAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTACAt < 1:1610245/70‑1 (MQ=255)
gTCGCGTTCAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAgg > 1:1773629/1‑71 (MQ=255)
cAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTAc > 1:4112660/1‑53 (MQ=255)
cAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTa > 1:1385460/1‑71 (MQ=255)
gTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTACATACCGCAgg > 1:2135947/1‑58 (MQ=255)
gTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTACATACCGCAgg > 1:2033340/1‑58 (MQ=255)
gTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATa > 1:3717147/1‑51 (MQ=255)
gTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATa > 1:1994006/1‑51 (MQ=255)
gTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACtt < 1:3494609/71‑1 (MQ=255)
tCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTACATACCGc > 1:3142900/1‑53 (MQ=255)
tCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTAc > 1:3510194/1‑71 (MQ=255)
tCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTAAATACCGCAGGCTGCGGTACACTTAc > 1:1611385/1‑71 (MQ=255)
tCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTAc > 1:2424166/1‑71 (MQ=255)
gcgGGTCCGCCCCGCTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGt < 1:116844/71‑1 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGTCGTTACATACCTCAGGCTGCGGTACACTTACCGTCTGTTGCTGa > 1:2434582/1‑71 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGt > 1:729809/1‑65 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGt > 1:3262746/1‑65 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGt > 1:592518/1‑65 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGt > 1:284180/1‑65 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGt > 1:1875560/1‑65 (MQ=255)
ccGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGa > 1:4056893/1‑71 (MQ=255)
cccGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACcat < 1:3466371/71‑1 (MQ=255)
cccGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACcat < 1:2028176/71‑1 (MQ=255)
ccGCTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGa > 1:3401911/1‑66 (MQ=255)
ccGCTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGa > 1:3294344/1‑66 (MQ=255)
cGCTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACcatca < 1:2354184/71‑1 (MQ=255)
gCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACcatcat > 1:1613211/1‑71 (MQ=255)
gCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACcatcat > 1:1245232/1‑71 (MQ=255)
gCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACcatca > 1:262479/1‑70 (MQ=255)
gCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGATg > 1:3800459/1‑60 (MQ=255)
cTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTg < 1:3872938/56‑1 (MQ=255)
cTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTg < 1:4017688/56‑1 (MQ=255)
cTAATTTCAACTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTg < 1:693699/56‑1 (MQ=255)
aTTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGc < 1:541252/70‑1 (MQ=255)
ttCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGtt > 1:4060512/1‑53 (MQ=255)
ttCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTg > 1:2355736/1‑71 (MQ=255)
ttCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTg > 1:3886748/1‑71 (MQ=255)
cAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGt < 1:2393469/70‑1 (MQ=255)
aaCTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTa < 1:2205519/70‑1 (MQ=255)
aCTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTACa < 1:1209075/71‑1 (MQ=255)
aCTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTACa < 1:478895/71‑1 (MQ=255)
aCTATAGGGTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTACa < 1:3412174/71‑1 (MQ=255)
aCTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTAc < 1:2829167/70‑1 (MQ=255)
aGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGATGACCATCATCGCTTGTACATGCcg > 1:1209158/1‑71 (MQ=255)
gggTCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTg > 1:3469137/1‑44 (MQ=255)
gggCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTACATGCcgc > 1:2263425/1‑71 (MQ=255)
|
CCTGATTTGCCGTCGCGTTCAGTGGTTCGAAACGCGGGTCCGCCCCGCTAATTTCAACTATAGGGCCGTTACATACCGCAGGCTGCGGTACACTTACCGTCTGTTGCTGACCATCATCGCTTGTACATGCCGC > minE/402585‑402717
|
| 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
