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 |
|
A1 F14 I0 R1
|
248 |
61.6 |
2601574 |
98.7% |
2567753 |
146.9 |
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 | 80.8%
| 56.6
/ 11.7
| 26 | 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 . (1/4); new base G (6/15); total (7/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 80.8%
| 55.4
/ 12.0
| 26 | 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 . (1/4); new base A (5/15); total (7/19) |
| 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: Variant not supported by required number of reads on each strand. |
CTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGC > NC_002947_CJ‑RC/1070099‑1070381
||
cTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑tgt > 6:170737/1‑148 (MQ=255)
aCGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑aga < 8:146511/149‑3 (MQ=255)
gccgATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑agatcgag < 5:64947/149‑8 (MQ=255)
aTTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGcgcc > 8:235631/1‑149 (MQ=255)
cATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCcgcgcg < 5:170737/149‑1 (MQ=255)
aTCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑tgt‑‑g > 3:122457/1‑131 (MQ=255)
aTCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑tgt‑‑g < 4:122457/131‑1 (MQ=255)
ggTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCgcgggcgg < 8:34535/148‑1 (MQ=255)
aaTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCt > 7:178808/1‑149 (MQ=255)
aTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTc < 1:228917/149‑1 (MQ=255)
aTGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTc < 5:246726/149‑1 (MQ=255)
tGCTGATCCCGGCATGGATCGCTGTGCTGGGGGTGGCTTTCAAGCTTAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGCTTTCATCGCC‑‑TGTGAG‑‑A‑‑GCGACCGCCGCCCGCGCGGCGCTCg < 1:512/149‑1 (MQ=25)
cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCCCGCGCGGCGCTCGa < 5:318123/148‑1 (MQ=38)
aTCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGAtct < 8:178808/148‑1 (MQ=255)
ggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGGG‑‑A‑‑TAGCGCGCCGCGCGGGCGGGGGGGGCTGCCCCCGGCGCTGAAAGCCTAAAgggctt > 2:22572/1‑145 (MQ=255)
ggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCAATGAAAGCCTAAAGGCAt < 7:235631/148‑1 (MQ=255)
cTTTCAAGCTGAAGAAGGGTCGCCAGGCCAAGGGCTGTTGGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCt < 2:90985/149‑1 (MQ=38)
tttCGAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGGGCGCCCCGCGGGGGGCGCGCGATCGCACAGGCGCTGCCAGCCGAAATGCAAGCgggtg > 6:77941/1‑145 (MQ=255)
ttCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TAGAGCGCCGCGCGGGCGGCGGTGGGTGTCACAGGCGATGAAAGCCTAAAAGCAAGCGTCTgg > 2:51495/1‑149 (MQ=38)
gCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCAGTGA‑‑G‑‑A‑‑TAGAGCGCCGCGCCGGCGGCGCTCGATCTGACAGGCGAAGAAAGCCAAAAGGCATTCGTCTGGCGGcc > 8:23007/1‑149 (MQ=255)
gCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGtt < 8:246193/149‑1 (MQ=255)
gCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TAGAGCGCCCCGCGGGCGGCGCGCGCTATCACAGGCGCTGAAAGCCTAAAGGGATTCGTCTGGGGGCCCGGGCGCGTTgccc > 6:97413/1‑149 (MQ=255)
cTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGTGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTc < 1:212215/149‑1 (MQ=255)
aTCGGGGTTGTTCGTAAGGGGAATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑AGCTCGAGCGCCGCGCTGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCa < 8:112996/147‑1 (MQ=38)
cGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGc < 2:113050/148‑1 (MQ=255)
atggggTATGCCTTTTGTTTTTCGGCGCC‑‑TGT‑‑GATA‑‑TCCCGCGCCGCGCGGGCGGCGCGCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa < 5:202077/146‑1 (MQ=255)
ggTTTTCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTa < 4:73674/149‑1 (MQ=255)
ttCGGCGCC‑‑TGTGAG‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAg < 7:23007/148‑1 (MQ=255)
gcGGCGCC‑‑TGTGAG‑‑A‑‑GCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGc < 1:302923/147‑1 (MQ=255)
||
CTGACGCCGCCGATTCGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCC‑‑TGT‑‑G‑‑A‑‑TCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGC > NC_002947_CJ‑RC/1070099‑1070381
|
| 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
