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 |
|
A3 F14 I0 R1
|
206 |
76.7 |
3255580 |
98.8% |
3216513 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,258,571 |
C→G |
39.0% |
intergenic (+20/+25) |
PP_5703 → / ← PP_4634 |
type III effector protein HopJ/alpha/beta family hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,258,571 | 0 | C | G | 39.0%
| 18.8
/ 4.9
| 20 | intergenic (+20/+25) | PP_5703/PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
| Reads supporting (aligned to +/- strand): ref base C (3/9); new base G (2/6); total (5/15) |
| 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 |
CGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATTTC > NC_002947_CJ‑RC/5258425‑5258715
|
cGGCGAGCACTACCGTAATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑TTTGc < 4:315378/147‑1 (MQ=255)
ggCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑TTTGCgg < 6:272294/148‑1 (MQ=255)
cGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑AAAGCGGcc > 7:343850/1‑148 (MQ=255)
aGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑TTTGCGGCCCCa < 1:50604/149‑1 (MQ=255)
gTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGAATGGCTTGAGATTGCCGGGG‑CCGC‑TTTGCGGCCCCACGATCCTg < 6:141742/148‑1 (MQ=255)
cGTCCACTGATCAAACCGGGGCTGGGGGGCTTTATGTTGGCTGCGCAGCGGCTGGGGCGCATGGTTTTATTTTGCCGGGG‑CCGG‑TTTGGGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTcc < 6:278654/147‑1 (MQ=255)
gtccACTGATCAACCACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAg < 8:342413/145‑1 (MQ=255)
gTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGTGG‑CCCC‑GTTGGGGGCCCCCCCTCCAGCGCCCCCCCACAAAACATGATGGTGCCAGGCccccccccaaaccgc > 2:84265/1‑142 (MQ=255)
tCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCCCGTTTGGGGCCCC‑CCAAACGGCGCCCCCCCCCAAAACCTGAATGTGCCCGGCCCCCCCCCAGCCACCCAccccag > 6:213281/1‑146 (MQ=255)
cgggcgTTAAGTTTGCTGCGCAGCCGCTTGCGCGAAAGGCTTTATATTGCGGGGG‑CCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCaa < 6:316206/148‑1 (MQ=255)
ggcgTTAAGTTTGCTGCGCAGCGGCTTGCGCGCATGGGTTTAGATTGCCGGGG‑CCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAgg < 6:172669/148‑1 (MQ=255)
ggcgcgaATGGATTCATATGGCGGGGG‑CCGA‑TTTGGGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGaaa < 7:139706/146‑1 (MQ=255)
gccaaaGGCTTTAGATGCCCGGGG‑CCCC‑TTTCGGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCgg < 7:17792/144‑1 (MQ=255)
gatttGCCGGGGCCCGG‑TTGGGGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGaaaaa < 2:149002/145‑1 (MQ=255)
gaTTGCCGGGG‑CGCA‑TTTCCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGTCTTTCGCGAAACCGGTCATGGAAAAAcgc < 1:42763/149‑1 (MQ=255)
tttGCGGGGG‑CGGT‑TTGGGGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAAcg < 7:285941/146‑1 (MQ=255)
ggg‑CCGC‑TTTGGGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATgg < 8:133891/148‑1 (MQ=255)
ccGT‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGACCaa < 4:265212/149‑1 (MQ=255)
ccGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGcc > 6:363090/1‑147 (MQ=255)
gC‑TTTGCGGCCCCACGATCCTACGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAt < 8:215322/148‑1 (MQ=255)
ttGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGGCATGGAAAAACGCGAAATGGCCAATTTc > 7:320211/1‑148 (MQ=255)
|
CGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGG‑CCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATTTC > NC_002947_CJ‑RC/5258425‑5258715
|
| 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
