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 R1
|
71 |
95.7 |
2922988 |
91.7% |
2680379 |
65.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,385,148:1 |
+T |
100% |
coding (651/1992 nt) |
cirA ← |
ferric iron‑catecholate outer membrane transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,385,148 | 1 | . | T | 96.9%
| 100.6
/ ‑2.3
| 32 | coding (651/1992 nt) | cirA | ferric iron‑catecholate outer membrane transporter |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (31/0); total (31/1) |
| Fisher's exact test for biased strand distribution p-value = 3.12e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-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. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
GCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAG‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTA > minE/1385088‑1385218
|
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:267875/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1694219/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1889118/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1896572/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1946273/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2131829/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2249744/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2405164/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:247876/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2532731/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2572554/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2586016/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2305966/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:268024/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2730342/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2746969/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2764744/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2790977/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:2869128/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:703580/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:748697/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:959191/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:980633/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1130753/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1331998/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1316148/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:124055/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1237642/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1205969/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1184534/1‑71 (MQ=255)
gCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAGTTTTTGCggg > 1:1077018/1‑71 (MQ=255)
tttCTCCGGTATCGGTGGTCGTTGAG‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCt < 1:365661/71‑1 (MQ=255)
g‑TTTTGCGTGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1746364/71‑1 (MQ=255)
g‑TTTTGCGGTTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1583769/71‑1 (MQ=255)
g‑TTTTGCGGTTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1587125/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2797160/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:110184/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:316041/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:346694/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:647354/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:457352/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:467303/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:619330/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1061809/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:680680/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1099816/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:713646/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1088993/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:776972/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:798305/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:877691/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:927203/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:942956/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:949820/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1595850/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2305210/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1603738/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1746765/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1753955/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1506553/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1939394/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1418920/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2009154/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1363516/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2140532/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1341696/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:115824/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1060937/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2311203/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2314770/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:234634/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2349880/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1337707/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2566745/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1284014/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:2603656/71‑1 (MQ=255)
g‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTa < 1:1181288/71‑1 (MQ=255)
|
GCCGTCGCGGCTGGAGAATCCTTCAATACGCGGCGTTTCTCCGGTATCGGTGGTCGTTGAG‑TTTTGCGGGTCATCCTTTTCACGTTTTGCCAGGCTGCCGTAAGCTTTCATTCCCAGCACACCATCAATTA > minE/1385088‑1385218
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
