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 |
1,463,378 |
C→T |
64.3% |
R273R (CGG→CGA) |
yfaA ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,463,378 | 0 | C | T | 64.3%
| 32.9
/ 31.5
| 56 | R273R (CGG→CGA) | yfaA | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (11/9); new base T (26/10); total (37/19) |
| Fisher's exact test for biased strand distribution p-value = 2.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTC > minE/1463327‑1463443
|
ccAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAAcc < 1:643201/68‑1 (MQ=255)
ccAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAAcc < 1:2073859/68‑1 (MQ=255)
ccAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAAcc < 1:2077861/68‑1 (MQ=255)
ccAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAAcc < 1:1663821/68‑1 (MQ=255)
ccAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAAcc < 1:2438424/68‑1 (MQ=255)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCg > 1:3030890/1‑39 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1907369/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1013190/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2032747/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2071380/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2183780/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2356757/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:26249/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2642119/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2833567/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:2934017/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:3020692/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:3157397/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:322953/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:3256621/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:3386412/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:456270/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1312418/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:132824/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1301100/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1871417/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1760597/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1717150/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1887655/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1359323/1‑40 (MQ=38)
cATTTCGAAGCGCACGCCAGCAAAAGAAGGCATTAATCGc > 1:1211556/1‑40 (MQ=38)
tCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACt > 1:1126727/1‑69 (MQ=255)
tCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACt > 1:1280340/1‑69 (MQ=255)
aaGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTAc < 1:880435/68‑1 (MQ=255)
aaGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTAc < 1:3292009/68‑1 (MQ=255)
aaGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTAc < 1:1160543/68‑1 (MQ=255)
tACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATgcg > 1:1954075/1‑69 (MQ=255)
tACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATgcg > 1:2565532/1‑69 (MQ=255)
cGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCt > 1:1779000/1‑69 (MQ=255)
cGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCt > 1:1007841/1‑69 (MQ=255)
aGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCg < 1:2263195/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGTCGCTGACTACGATGCGCTGGCGTa < 1:3348247/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:1026747/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:2649495/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:2740038/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:2720047/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:1399053/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:1400057/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:1599103/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:1804053/69‑1 (MQ=255)
cAAAAGAAGGCATTAATCGCTGGTAGCCAAACCCCAGCAACCTGGCGCTGACTACGATGCGCTGGCGTa < 1:2021605/69‑1 (MQ=255)
aaCCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTc > 1:1327282/1‑68 (MQ=255)
aaCCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTc > 1:2512461/1‑68 (MQ=255)
aaCCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTc > 1:1965686/1‑68 (MQ=255)
aaCCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTc > 1:1958983/1‑68 (MQ=255)
aaCCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTc > 1:894784/1‑68 (MQ=255)
|
CCAGCCGTCGTTACCCATTTCGAAGCGTACGCCAGCAAAAGAAGGCATTAACCGCTGGTAGCCAAACCCCAGCCACCTGGCGCTGACTACGATGCGCTGGCGTACTGGCGTTTTTTC > minE/1463327‑1463443
|
| 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
