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 I0 R1
|
140 |
52.5 |
2164708 |
98.8% |
2138731 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,070,246:1 |
+GA |
100% |
intergenic (+46/+96) |
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 | 84.6%
| 23.5
/ ‑4.4
| 15 | 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 . (1/1); major base G (1/10); minor base C (0/2); total (2/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 86.7%
| 27.6
/ 2.3
| 15 | 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 . (1/1); new base A (1/11); total (2/13) |
| Fisher's exact test for biased strand distribution p-value = 2.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.24e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑T‑‑GATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTA > NC_002947_CJ‑RC/1070148‑1070377
||
cggggcggtggggggCTTTCAAGCTGACTACGGCTCGCCAGCCCAAGGGCTGATCGGGTTTGTTCGAAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGGG‑‑A‑‑GAGCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAg < 4:190219/140‑1 (MQ=25)
gtgggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAg > 2:25950/1‑147 (MQ=255)
ggtggCTTACACGCTTAAGACGGCGCGCCCGCCAATGGGGTGTGGGGGTTTGTTCGTACGGGTTTGCCCTTTTGTTTTTCGCCGCCG‑‑G‑‑TCCCACCCCCCCCCGGGCGGGCGGCGCTGTATCTCACAGGCGATGAAAGCCTAAAGGCa < 6:33701/147‑1 (MQ=255)
cTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTTGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGt < 2:185393/147‑1 (MQ=255)
cTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTggcggc < 2:169337/147‑1 (MQ=255)
cTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTAGGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCCCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTggcggc < 2:109612/147‑1 (MQ=38)
agaagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑GTTT‑‑GATAGAGCGCCCCGCGGGCGGGGCGGGGGGTCACCAGCGCTGAAAGCCTAAACGCCTTCGGCTGGCGGgccgg > 6:87172/1‑145 (MQ=255)
gaagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGa < 2:214355/147‑1 (MQ=255)
gaagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TCAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGa < 1:25950/147‑1 (MQ=255)
gCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTc < 6:66276/147‑1 (MQ=255)
cAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCa < 4:84842/147‑1 (MQ=255)
ggTTTGTTCGTAAGGGTTTTGCCGTTTGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGTGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtg < 6:129826/146‑1 (MQ=38)
gTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgt < 6:144621/147‑1 (MQ=255)
gTTAGGTTTTCGGCGCCT‑‑G‑‑TGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgt < 8:136226/147‑1 (MQ=255)
ttttGGGCGCCT‑‑G‑‑GGAGATCGCGCGCGGCGCGGGCGGCGGTCTATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTa < 4:70985/147‑1 (MQ=255)
||
CTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCT‑‑G‑‑T‑‑GATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTA > NC_002947_CJ‑RC/1070148‑1070377
|
| 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
