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 |
1,523,658 |
C→T |
48.6% |
Q153* (CAA→TAA) |
flk → |
predicted flagella assembly protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,523,658 | 0 | C | T | 48.6%
| 1.6
/ 50.3
| 37 | Q153* (CAA→TAA) | flk | predicted flagella assembly protein |
| Reads supporting (aligned to +/- strand): ref base C (12/7); new base T (11/7); total (23/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AATCAGCTCTCACCGGAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGCACAATGCGCTAAAACAGCT > minE/1523589‑1523725
|
aaTCAGCTCTCACCGGAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGc < 1:915494/70‑1 (MQ=255)
aaTCAGCTCTCACCGGAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGc < 1:512708/70‑1 (MQ=255)
tcACCGGAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCAcag > 1:454330/1‑69 (MQ=255)
aCCGGAGCAATTAAAAACCATTCTCACCCTGTTGGAGGAAGGGAAGATGGTTATTCCGTAACCAcagcag > 1:320897/1‑70 (MQ=255)
aCCGGAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCAcagc < 1:526308/68‑1 (MQ=255)
ggAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGc < 1:550291/56‑1 (MQ=255)
ggAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAgcgc > 1:1357755/1‑70 (MQ=255)
gCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCAGCAACCACAGCAGCGCGAgg < 1:771779/71‑1 (MQ=255)
ttAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGc < 1:695435/49‑1 (MQ=255)
ttAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGcg < 1:1539270/69‑1 (MQ=255)
ttAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGcgac > 1:994006/1‑71 (MQ=255)
ttAAAAACAATTCTCACCCTGTAGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGcg < 1:1055413/69‑1 (MQ=255)
tAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGcgac > 1:1814360/1‑70 (MQ=255)
aagaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGcgacc > 1:948499/4‑70 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGcgacc > 1:1852275/1‑70 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCATCGCGAGGcgacc > 1:1992110/1‑70 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGa > 1:747416/1‑63 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGa > 1:315601/1‑63 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAgg > 1:523158/1‑65 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGcgacc < 1:1253614/70‑1 (MQ=255)
aaaaaCCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGc > 1:1679198/1‑66 (MQ=255)
aCCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCttt < 1:2188004/68‑1 (MQ=255)
aCCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCttt < 1:1919177/68‑1 (MQ=255)
aCCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTttat > 1:1823542/1‑70 (MQ=255)
ccTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTAc > 1:1175517/1‑71 (MQ=255)
ccTGTTGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTAc > 1:2035066/1‑71 (MQ=255)
tGCAGGAAGGGAAGATGGTTATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTAc > 1:2132338/1‑66 (MQ=255)
tGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGAGCGAGGCGACCGACCGTCCTTTATTACcggcg > 1:1108805/1‑71 (MQ=255)
gCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTtta > 1:1856255/1‑61 (MQ=255)
gaagggaagATGGTTATTCCGTAACCACAGCAGCGCGAGGCCACCGACCGTCCTTTATTACCGGCGGAGca > 1:421135/1‑71 (MQ=255)
aagggaagATGGTTATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGcac < 1:79231/71‑1 (MQ=255)
aagggaagATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGcac < 1:1874337/71‑1 (MQ=255)
aagggaagATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGcac < 1:1656218/71‑1 (MQ=255)
aagggaagATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGcac < 1:466379/71‑1 (MQ=255)
gggaagATGGTTATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGCACaa < 1:491673/71‑1 (MQ=255)
ggaagATGGTTATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGcac < 1:1762032/68‑1 (MQ=255)
ggTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGCACAATgcgc > 1:2166844/1‑68 (MQ=255)
ttATTCCGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGcac < 1:1937321/59‑1 (MQ=255)
tATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGCACAATg > 1:230711/1‑62 (MQ=255)
tCCGTAACCACAGCAGCGCGAGGCGACCGACCGTGCTtta > 1:584855/1‑40 (MQ=37)
ccGTAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGCACAATGCGCTAAAACAGCt > 1:915968/1‑71 (MQ=255)
|
AATCAGCTCTCACCGGAGCAATTAAAAACCATTCTCACCCTGTTGCAGGAAGGGAAGATGGTTATTCCGCAACCACAGCAGCGCGAGGCGACCGACCGTCCTTTATTACCGGCGGAGCACAATGCGCTAAAACAGCT > minE/1523589‑1523725
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
