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 |
|
A13 F1 I2 R1
|
762 |
35.5 |
1545288 |
95.5% |
1475750 |
117.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,664,096 |
T→C |
I163T (ATA→ACA) |
ynfH → |
oxidoreductase, membrane subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,664,096 | 0 | T | C | 97.1%
| 118.2
/ ‑4.8
| 35 | I163T (ATA→ACA) | ynfH | oxidoreductase, membrane subunit |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (17/17); total (17/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
GGTTACTTTTCAGCATGGCGCTCGGCGTCATTTTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAATACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCTATTCA > NC_000913/1663958‑1664228
|
ggTTACTTTTCAGCATGGCGCTCGGCGTCATTTTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAAt > 2:9012/1‑139 (MQ=255)
ggCGCTCGGCGTCATTTTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAAtt > 2:210076/1‑139 (MQ=255)
ggCGCTCGGCGTCATTTTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAAtt > 1:507241/1‑139 (MQ=255)
cATTTTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCTTTCTTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCa > 1:91292/1‑139 (MQ=255)
ttCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTcgcg < 1:697857/139‑1 (MQ=255)
cGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGtt < 1:96370/139‑1 (MQ=255)
cGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGtt < 1:336053/139‑1 (MQ=255)
cGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGtt < 2:507241/139‑1 (MQ=255)
ggATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAtt < 1:585768/139‑1 (MQ=255)
gatgatGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAttt > 2:608333/1‑139 (MQ=255)
aCCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACca > 1:142563/1‑139 (MQ=255)
tGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCacac > 2:313133/1‑139 (MQ=255)
cGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCa > 2:651676/1‑139 (MQ=255)
tCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGcc < 1:608333/139‑1 (MQ=255)
tGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGtt > 2:497356/1‑137 (MQ=255)
tGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGtt < 1:497356/137‑1 (MQ=255)
gCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTGGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATc > 2:544513/1‑139 (MQ=255)
cTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGt < 1:544513/139‑1 (MQ=255)
cGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGa < 1:130850/120‑1 (MQ=255)
cGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGa > 2:130850/1‑120 (MQ=255)
cGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGAt > 2:418777/1‑139 (MQ=255)
gCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAATACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGAtt < 1:9012/139‑1 (MQ=255)
gCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGAtt < 1:210076/139‑1 (MQ=255)
gCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGa > 2:370308/1‑133 (MQ=255)
gCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGa < 1:370308/133‑1 (MQ=255)
cttcCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCg > 1:770768/1‑98 (MQ=255)
cttcCTGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCg < 2:770768/98‑1 (MQ=255)
tGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAtt < 1:83966/64‑1 (MQ=255)
tGACGGTATTGTTGAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACAtt > 2:83966/1‑64 (MQ=255)
gttgAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCg < 1:651676/139‑1 (MQ=255)
ttgAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGt < 2:91292/139‑1 (MQ=255)
tgAGCGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCG‑TCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCt < 1:458974/139‑1 (MQ=255)
cGGTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCTAtt > 1:705216/1‑139 (MQ=255)
gTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGc < 1:554291/91‑1 (MQ=255)
gTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGc > 2:554291/1‑91 (MQ=255)
gTCCAACACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCTATTCa > 1:207920/1‑139 (MQ=255)
|
GGTTACTTTTCAGCATGGCGCTCGGCGTCATTTTCGTCTGGATGATGACCTGCGTGTATCAAATCGACACCGTGCCAACCTGGCATAACGGTTACACTACGCTGGCT‑‑‑TTCTTCCTGACGGTATTGTTGAGCGGTCCAATACTTGCTGCCGCAATTCTGCGGGCAGCTCGCGTTACATTTAATACCACACCATTTGCCATCATTAGCGTTCTGGCGCTGATCGCTTGTGCCGGGGTGATTGTGCTGCAAGGTTTGTCTCTGGCGTCTATTCA > NC_000913/1663958‑1664228
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
