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 F13 I1 R1
|
59 |
72.5 |
3655346 |
98.4% |
3596860 |
137.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,070,248 |
+GA |
intergenic (+48/+94) |
aroP‑I → / ← PP_0928 |
aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 76.2%
| 40.8
/ 13.1
| 22 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| Reads supporting (aligned to +/- strand): ref base . (2/3); new base G (6/10); total (8/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.49e-01 |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 76.2%
| 42.8
/ 13.7
| 22 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| Reads supporting (aligned to +/- strand): ref base . (2/3); new base A (6/10); total (8/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.75e-01 |
GATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑GA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTAC > NC_002947_CJ‑RC/1070110‑1070378
||
gATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAgcgc > 3:392361/1‑149 (MQ=255)
tGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTc > 6:68843/1‑148 (MQ=255)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGAt < 3:77748/149‑1 (MQ=255)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGAt < 4:392361/149‑1 (MQ=255)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGAt < 5:68843/149‑1 (MQ=255)
aTCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑Gagatcga < 8:470724/123‑7 (MQ=255)
aTCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑Gagatcga > 7:470724/1‑117 (MQ=255)
tCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGAtctc < 2:278765/148‑1 (MQ=255)
aTCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑AGACCCCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGa > 6:347648/1‑148 (MQ=39)
ggggttgggggggCTTTAATGCTTATGAAGGCTGGCCTGGCAACGGGCTTATGGGGTTTGTTCGTATGGGGTAGCCCTTTTGGTTTTCGGCGCGTGTTCGT‑T‑CGCGCGCCGCGGGGGCGGGGCTGTATCTCACAGGCGATGAAAGCCt < 6:249015/141‑1 (MQ=255)
ctgtgGGTGGATTTCAAGCTTAACACGGCGCGCCTGGCCATGGGCTTTTGGGTTTTGTTCTTACGGGTTATGCGTTTTGTTTTTGGGCGCCTGTGAGA‑T‑CGCGCGCGGCGCGGGCGGCGCTCTATCTCACAGGCGATGAAAGCCTaa < 2:217295/147‑1 (MQ=255)
aaGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTTGGTTTTCGGCGCCTGTGAGA‑T‑CGCGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTggcg < 2:143862/148‑1 (MQ=38)
aaGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTggcgg > 6:353460/1‑149 (MQ=255)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCCCGCGCGGCGCTCGa < 7:469716/98‑1 (MQ=25)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCCCGCGCGGCGCTCGa > 8:469716/1‑98 (MQ=25)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑Ga < 7:348078/70‑1 (MQ=255)
ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑Ga > 8:348078/1‑70 (MQ=255)
aaGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGTGCGCCGCGGGGGCGGCGCTGGATCTCACAGTCGATGAAAGGCTATAGGCATGGGTCTGGCGGCCCTGACGCGTTCCCCTTGCaagt > 8:207749/1‑146 (MQ=37)
gCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCt < 5:353460/149‑1 (MQ=255)
ggttATGCCTTTAGTTTATCGGCGCCTGTGAGA‑T‑CTAGCGCCGCGCGGGCGGCGCTCGATCTCACAGTCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAgcac < 7:207749/146‑1 (MQ=38)
gTTTTCGGGGCCTGT‑‑CAGTACGAGCGCGGGGGGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCAAGCCCCTCAATGCTGCCTCCGCCAAgcacgc < 7:429092/137‑1 (MQ=255)
gTTTTCGGCGCCTGTGAGA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTAc < 5:365209/149‑1 (MQ=255)
||
GATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGT‑‑GA‑T‑CGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTAC > NC_002947_CJ‑RC/1070110‑1070378
|
| 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
