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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,530,201 |
G→A |
100% |
G204G (GGC→GGT) |
yfcA ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,530,201 | 0 | G | A | 97.5%
| 79.3
/ ‑5.1
| 37 | G204G (GGC→GGT) | yfcA | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (18/17); total (19/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GGAACTGCCCCACCAGCATGACAAAGCCCGTCGCCCAAATCACTTTGCCGCCGAGAATAAACAGCAGTAAACCGCCGATGTTTGACGTTGCGTTGAGTAATTTGGCGTGAGC > minE/1530152‑1530263
|
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCCCCgaga > 1:2883605/1‑56 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:995878/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:1045303/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:883012/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:697596/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:39789/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:348363/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:3342856/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:3289835/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:3226122/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:3055395/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:2884694/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:2638091/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:1162714/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:1926696/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:1905094/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:1896842/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:2500953/1‑67 (MQ=255)
ggAACTGTCCTACCAACATCACAAATCCTGTCGCCCAAATCACTTTGCCACCGAGAATAAAcagcagca > 1:1732022/1‑67 (MQ=255)
ccAAATCACTTTGCGACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:2648232/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCTGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:3190963/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1736804/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1410507/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:823294/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:763111/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:513196/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:507323/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:483483/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1644227/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1784644/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:3057616/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1904919/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1911239/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:2863955/68‑1 (MQ=255)
ccAAATCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:2543129/68‑1 (MQ=255)
aaTCACTTTGCCACCGAGAATAAACAGCAGCAAACCGCCAATGTTTGACGTTGCGTTAAGTAAtt < 1:1636599/65‑1 (MQ=255)
tttGCCGCCGAGAATAAACAGCAGTAAACCGCCGATGTTTGACGTTGCGTTGAGTAATTTGGCGTGAGc < 1:34928/69‑1 (MQ=255)
|
GGAACTGCCCCACCAGCATGACAAAGCCCGTCGCCCAAATCACTTTGCCGCCGAGAATAAACAGCAGTAAACCGCCGATGTTTGACGTTGCGTTGAGTAATTTGGCGTGAGC > minE/1530152‑1530263
|
| 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
