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 |
5,258,571 |
C→G |
24.8% |
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 | 24.8%
| 47.3
/ 2.7
| 27 | intergenic (+20/+25) | PP_5703/PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
| Reads supporting (aligned to +/- strand): ref base C (5/14); new base G (3/4); total (9/18) |
| Fisher's exact test for biased strand distribution p-value = 6.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATTTCCT > NC_002947_CJ‑RC/5258429‑5258717
|
gAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGcc < 4:192469/147‑1 (MQ=255)
aGCACTACCGTGATGTGTTGGCCACGCCTGTGGGTAGCGACGATTGCAACATCCGTGCACTGATCTAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCTAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGccc < 2:147868/147‑1 (MQ=255)
aGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGccc < 8:190694/147‑1 (MQ=255)
gCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGcccc < 4:130257/147‑1 (MQ=255)
gCACTACCGTGATGTGTCGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGcccc < 1:222703/147‑1 (MQ=255)
aCCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGGCGCGTTTGGGGcccaccc > 6:17912/1‑142 (MQ=255)
tGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGGCGCGTTTGGGGCCCC‑CGCTCCGGCGCCCCCCCACCAACCat > 6:43483/1‑147 (MQ=255)
cGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGACTTGAGATTGCCGGGGCCGC‑TTTGAGGCCCCCCGAACCTGCGCCCACCCAGAATGCATGATGGTg > 8:267733/1‑145 (MQ=255)
cATCCGTGCACTGATCAAACACGGTCTGGAGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTTGCGCCCCACGATCCTGCCCCCACCCGAAAAACATTATGGTGCCCGGCcccccccc > 6:262417/1‑147 (MQ=255)
tCTGGCGGGCTTTAAGTTTGCTGCGCAGCCGATTGCGCGCATGGTTTGTTTTTGCGGGGGCCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCa < 8:49458/147‑1 (MQ=255)
ggggcgTTATTTTTGCGGCGCCGCGGTTGGCGCGAATGGCTTTATATGGCCGGGGCCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCa < 1:150264/146‑1 (MQ=255)
tttttGCGGCCCCGCCGCTGGCGCTAATGGTTTTATATGGCGGGGGCCGT‑TTGGCGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCAcc < 5:231233/144‑1 (MQ=255)
gTTTGCTGCGCCGCCGCTGCCGCTAATGGCTTGAGATTGCCGGGGCCGG‑TTTGGGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCgg < 7:157506/147‑1 (MQ=255)
cAAGGCTTGAGATTGCCGGGGCCCC‑GATTCGGCCCCACCATACAGCGCCCCCCCGCAAAACATGATGGTGCCAGGCCCCCCCCCATACCGCCACCCCAGCCGCAACCACAGCAAAGCCCCCGGCCACACGCATTCGCGaaaaccgg > 2:162076/1‑141 (MQ=255)
aaGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCa < 2:3009/147‑1 (MQ=255)
ggCTTGTGATTGCGGGGGCCGC‑TTTGGGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATg < 2:176823/147‑1 (MQ=255)
gaTGGCGGGGGCCGA‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGaaaaa < 7:72828/146‑1 (MQ=255)
atggCCGGGCCCGC‑TTGGGGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAAcg < 7:65828/144‑1 (MQ=255)
ggCCGGGGCCGC‑TTGGCGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAAcgc < 4:207259/145‑1 (MQ=255)
ggggCCGG‑TTGGGGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAAt < 5:132349/147‑1 (MQ=255)
gggcCCCC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAAt < 6:259295/147‑1 (MQ=255)
gggCCGC‑TGTGCGGCCCCACGATCCTGCTCCCACCCTCAATCCATGCTGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATg < 4:183444/147‑1 (MQ=255)
ggCCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCACCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATgg > 1:164530/1‑147 (MQ=255)
gcccGC‑TTGGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATgg < 6:228836/145‑1 (MQ=255)
c‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCCGCCCCCCCTGCCGCAACCACTGCAAGGCCACCGGCCTCAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAt > 3:96440/1‑147 (MQ=255)
c‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAt > 6:236236/1‑147 (MQ=255)
tGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGG‑CCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATTTcc > 2:33200/1‑147 (MQ=255)
cGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATTTCCt > 4:203789/1‑147 (MQ=255)
|
GAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGC‑TTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATTTCCT > NC_002947_CJ‑RC/5258429‑5258717
|
| 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
