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 F36 I0 R1
|
111 |
89.1 |
3136336 |
98.1% |
3076745 |
142.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,708,930 |
C→A |
20.7% |
P671Q (CCG→CAG) |
rsxC → |
SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,708,930 | 0 | C | A | 20.7%
| 53.3
/ 2.2
| 35 | P671Q (CCG→CAG) | rsxC | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| Reads supporting (aligned to +/- strand): ref base C (18/9); new base A (5/3); total (23/12) |
| 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 |
GCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTT > NC_000913/1708791‑1709075
|
gCCTCTATTTCCCGTGCCAAAGCACGCAATCTGTCTCAGCAAAAGGCTAATGCCGTGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGc < 7:55451/149‑1 (MQ=17)
gCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAgaagaa > 7:74603/1‑147 (MQ=255)
gCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTAGATCCGCGCAAAGCGGCAGTCGAAGCCGCTATTGCCCGCGCGCAAGCCCACAAAGGCGCACAGCACCCGGGTTAAGCCGAGCAAGATCAGCAGGTTGAGCCgcgc > 6:144033/1‑148 (MQ=9)
aCAGGCTAATGCCGAGCCAGAAAAACAGGTCGATCCGCGCAAAGCCGCAGTAGAAGCCGCTATTGCCCGAGCGAAAGCAATCAAACCCAAACAGAAAAAGGCAAATTCGGAGGAGGAAGAAAAAGCTCATACGAGCGAAGCTGCAGtg > 2:33013/1‑147 (MQ=2)
ccGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTAtt < 8:74603/149‑1 (MQ=255)
cGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCGCGCAAACGGGACCAGCAACAGGCTAATGCGGAGCCAGAAGACCAGGTTGATCCGCGCACAGCTGCAGTAGACGCGGCGATTg > 3:139761/1‑149 (MQ=14)
ccAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAGCGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGCGTGCTCCGCGCCACGCTGCCGACGAAGCGTCTAATCCAcg > 1:34144/1‑149 (MQ=14)
aGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAACGCGAGCAAACGCGAACAGCAACCGGATAATGCGGAGCCAGAAGAACAGGTTCATCCGCGCAAAGCTGACGTCGCCGCTGCTCTTGCCcgcg > 5:199526/1‑149 (MQ=14)
aGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACTGGAACAGCAACCGGCTaa > 2:77787/1‑87 (MQ=255)
aGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACTGGAACAGCAACCGGCTaa < 1:77787/87‑1 (MQ=255)
gaagaaCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCag > 2:355247/1‑97 (MQ=255)
gaagaaCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCag < 1:355247/97‑1 (MQ=255)
aacaGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAGCGGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTTGAt > 1:44467/1‑107 (MQ=255)
aacaGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACTGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGAt < 2:44467/107‑1 (MQ=255)
aacaGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGc > 5:243779/1‑79 (MQ=255)
aacaGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGc < 6:243779/79‑1 (MQ=255)
acaGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGACCAGGGTGCTGCGCGCAACGCTCCCGGCGCCGCGGCGATTGCTCGCGGCagcc > 5:185323/1‑146 (MQ=17)
aGGTCGATCCGCGCAAAGCCGCCGTAGAAGCCGCTATTGCCCGAGCAAAAGCAAGCAAACAGGAACAGCAACAGGCTAATGCGGATCCAGAAGATCAGGATGATCCGCGCAAAGAGGCAGTAGAAGAAGCTATTGCCCgcgcgcagggc > 4:230477/1‑142 (MQ=11)
gcgcAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGGTAGGGACCGGCCCAAAGCACgaactcag > 3:74203/1‑141 (MQ=14)
cAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTAGACGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGaa > 8:7114/1‑148 (MQ=255)
aaaGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGaa > 8:279026/1‑147 (MQ=255)
cgccgTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGACGTCGGAGCAGCTATTGCACGCGCCAAAGGAAGCAAGCGTGAACAGCaag > 2:383730/1‑148 (MQ=17)
gccgTCGACCCCGCTATCGCCCGATCCACCGCGCTCACCCGGTAACAGCACCCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACa < 3:13206/149‑1 (MQ=17)
gccgTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGACGCGGCTATTGCACGCGCCCAAGCACCCAACCGCGAACAGCaa > 7:386683/1‑147 (MQ=17)
cttttaaGCAGCTATTGCCCTCGCCAAAGCCCGCACGCGTTCACAGCAACAGGCTACTGCGGCCCCAGACGATCTGGTCGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAgg < 2:202530/144‑1 (MQ=11)
gCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTCGAAGCGGCTATTGCCCGCGCAAAGGCCCGCTAGCTGGAGCCGCGTCAGGGGAATGc > 8:324577/1‑149 (MQ=17)
aGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAAc < 7:279026/149‑1 (MQ=255)
cAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCCCGCGCAAAAGCCCGCAAGCAGGACCAGCAACACGCGAAGGCGGAACCAGAACAACAgg > 3:215981/1‑149 (MQ=21)
aaaGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCAGTAGAAGCGGCTATTGCACGCGCGAAAGCAATCAAGCTGGAACAGCAACAGGCTAATGCGCTACCAGAAGAACAGGt > 3:170245/1‑149 (MQ=18)
aaGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTAt < 2:375500/85‑1 (MQ=11)
tggAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTAGATCCGCGCAAAGCAGCCGTCGAAGCGGCTATTGCAcgcg > 4:271688/2‑81 (MQ=11)
aaccgcaaccgcCTAATGCGGAGCCAGAACACCCGGGTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCg < 1:383730/149‑1 (MQ=17)
cAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTgg > 1:157448/1‑91 (MQ=255)
cAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTgg < 2:157448/91‑1 (MQ=255)
cAACAGGCTAATGCGGAGCCAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCAc < 5:298596/82‑1 (MQ=255)
aaCCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCAAAAGCACGCAAGCTGGAACAGCAACAGGCTAAAGCGCTACCAGAAGAACAGGTTGATCCGCGCCAAGAGGCAGtt > 1:201915/1‑149 (MQ=18)
|
GCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTT > NC_000913/1708791‑1709075
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
