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 |
|
A4 F3 I0 R2
|
8 |
43.3 |
2136430 |
96.9% |
2070200 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,763,556 |
T→C |
40.3% |
noncoding (288/1542 nt) |
rrsG ← |
16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,763,556 | 0 | T | C | 40.3%
| 31.4
/ 68.0
| 57 | noncoding (288/1542 nt) | rrsG | 16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base T (15/19); new base C (16/7); total (31/26) |
| Fisher's exact test for biased strand distribution p-value = 1.03e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGC > minE/1763502‑1763624
|
ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCtt < 1:1665936/70‑1 (MQ=31)
ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCtt < 1:400527/70‑1 (MQ=14)
ggAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCtt < 1:1812578/70‑1 (MQ=14)
aGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGt > 1:19134/1‑71 (MQ=21)
tCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGa < 1:451838/71‑1 (MQ=34)
tCTGGACCGTGTCTCAGTTCCAGTGTGACTGATCATCCTCTCAGACCAGTTACGGATCGTCGCCTTGGTGa < 1:393430/71‑1 (MQ=11)
cTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAg > 1:130010/1‑71 (MQ=34)
acagtgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt > 1:1497165/4‑71 (MQ=21)
ccGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGt > 1:145556/1‑70 (MQ=35)
cGTGTCTCAGTTCCAGTGTGGCTGGTCGTCCTCTCAGACCAGCTACTGATCGTCGCCTTGGTGAGcctt < 1:1139543/69‑3 (MQ=11)
tgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcc > 1:1250149/1‑71 (MQ=34)
tgtCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAc < 1:1629028/70‑1 (MQ=35)
gtCACAGTTCCAGTGTGGCTGGTCATCCTGTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTAccc > 1:1935637/1‑71 (MQ=11)
tctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAccc > 1:1764118/1‑70 (MQ=35)
ctcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCcca > 1:284009/1‑71 (MQ=34)
tcAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCccac > 1:797423/1‑71 (MQ=21)
aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc > 1:1671498/1‑70 (MQ=35)
aGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCccacc > 1:2135057/1‑70 (MQ=35)
gtcccAATGTGGCTGATCATCCTCTCAGACCAGCTACTGATCGTCGCCTTGGTGAGCCAtt < 1:1218584/58‑1 (MQ=11)
ttCCAGTGTGGCTGGTCGTCCTCTCAGACCAGCTACTGATCGTCGCCTTGGTGAGCCTTTACCTCACcaac > 1:373570/1‑71 (MQ=14)
ttCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTgg < 1:580298/51‑1 (MQ=35)
ttCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac < 1:604336/71‑1 (MQ=39)
tCCAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac > 1:559577/1‑70 (MQ=255)
ccAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGcc > 1:326904/1‑55 (MQ=255)
ccAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac > 1:616620/1‑69 (MQ=255)
ccAGTGTGGCTGGTCATCCTCTCAGACCAGCCAGGCATCGTCGCCTTGGTGAGCCGTTAccc > 1:1313875/1‑62 (MQ=255)
gtgtGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGt > 1:1134826/1‑47 (MQ=255)
gtgtGGCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCt < 1:1450601/71‑1 (MQ=255)
gCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa > 1:618990/1‑68 (MQ=255)
gCTGGTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATc < 1:148132/70‑1 (MQ=255)
gTCATCCTCTCAGACCAGCTATGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATc < 1:2003371/71‑1 (MQ=255)
gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCa < 1:1107812/69‑1 (MQ=255)
gTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCAt < 1:1915691/70‑1 (MQ=255)
gTCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAg < 1:2053106/41‑1 (MQ=255)
tCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCt < 1:447726/71‑1 (MQ=255)
tCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAg < 1:920412/40‑1 (MQ=255)
tCATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCTTCt > 1:1770593/1‑71 (MQ=255)
cATCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGcc > 1:647133/1‑41 (MQ=255)
aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcccc > 1:924616/1‑48 (MQ=38)
aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAcccc > 1:548777/1‑48 (MQ=38)
aTCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa > 1:307187/1‑61 (MQ=255)
aTCCTCTCAGACAAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa > 1:1820755/1‑61 (MQ=255)
tCCTCTCAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTgg > 1:1463060/1‑70 (MQ=255)
ccTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTAc < 1:834535/43‑1 (MQ=38)
ctcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATc < 1:329499/58‑1 (MQ=255)
tcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaaca < 1:1647221/49‑1 (MQ=255)
tcAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaaca < 1:1343490/49‑1 (MQ=255)
tcAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAg > 1:890083/1‑51 (MQ=255)
cAGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATc > 1:1419288/1‑71 (MQ=255)
aGACCAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATcc > 1:946237/1‑71 (MQ=255)
aCCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACcaac < 1:242493/44‑1 (MQ=255)
aCCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGa > 1:54856/1‑71 (MQ=255)
cAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCccacca > 1:1342052/1‑40 (MQ=255)
cAGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa > 1:1443972/1‑49 (MQ=255)
aGCCAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTaa < 1:1466603/48‑1 (MQ=255)
gCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGc < 1:2060297/71‑1 (MQ=255)
cTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATc < 1:1014925/53‑1 (MQ=255)
|
GGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGC > minE/1763502‑1763624
|
| 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
