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 |
1,403,591 |
T→G |
33.8% |
intergenic (‑57/+24) |
PP_1227 ← / ← PP_1228 |
membrane protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,403,591 | 0 | T | G | 33.8%
| 22.3
/ 3.0
| 25 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base T (8/5); new base G (3/5); total (11/14) |
| Fisher's exact test for biased strand distribution p-value = 3.87e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATGAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCGGC > NC_002947_CJ‑RC/1403449‑1403737
|
aTGAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCcgc > 2:130124/1‑149 (MQ=255)
aaCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCATGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGa < 8:376985/148‑1 (MQ=255)
aaCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGaa < 1:29747/149‑1 (MQ=255)
aaCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTACGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGa < 5:357789/148‑1 (MQ=255)
cAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAaga < 2:156314/149‑1 (MQ=255)
cAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGAGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAaga < 3:259159/149‑1 (MQ=255)
gATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGC‑GGCGCTGACAgg > 2:243460/1‑149 (MQ=255)
aGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCAGTAAGGGCCACGTAACGGGCGGGGCCCCGGAGA‑AGCCCCGACAGGcgaaa > 4:280717/1‑145 (MQ=255)
cTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTATACGCGAAACTGCTc > 6:253238/1‑147 (MQ=255)
ttGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCGGTGAAGGGCACGTTGCGGGGGGGGCCCCGCAGAGGGCCCGGGCAGGGGTGACGCGaaaaaggcca > 4:60340/1‑141 (MQ=255)
cTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAgcgc > 8:295026/1‑148 (MQ=255)
gATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCg < 6:167007/148‑1 (MQ=255)
gATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCAGTCAGGGCCTCTTAGCGGGGGGGGCCGCGAATA‑GGGCCGGGCAGGCGAGACGCGGAACTGCTCCCAAAGCGCCGGCTGCGGGTTTGGCCGCCgg > 2:69772/1‑149 (MQ=255)
gtaTTCGGAATAAGTGGTGCCAAAGAAAAACGTGGGTGCGGGGCCTGGCCGGGCCGCTGCGCGGGGGGGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAggg < 5:118348/145‑1 (MQ=255)
tttttggCATATGTTGTGCTCATTAATATCGTTGGGGGGGTGCCTGTCCGGGCCTCTTGGCGGGCGTGCCCGCTAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCtt < 2:28409/144‑1 (MQ=255)
cATACGTTGTGCCCAATAAAACCGAGGGGGCGGGGCCTGCCCGGGCCTCTGCGCGGGCGGGCCGGCTAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGa < 5:330712/148‑1 (MQ=255)
aTACGTTGGGCCCAAGAAAACCGATGGTGCGGGGCCTGCCCGGGCCTCTACGCGGGCGCCCCCGCGAAGA‑GGCCCTGACAGGCTAGACTCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGAt < 6:104268/148‑1 (MQ=37)
gTTGTCCCCAATAAAAACGAGGGTCGGGTGCCGGCCAGGCCCTCTCCGCGGCCGGCCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGt < 7:222005/148‑1 (MQ=255)
ggtgcCTTTCCGGTCCTCTTGGGGGGCGGGCCCGCGAATA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCccagccag < 8:253531/148‑1 (MQ=255)
gggCCTCTTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCa < 5:171923/148‑1 (MQ=255)
tctTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGtctc > 1:187424/1‑149 (MQ=255)
tCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCg > 8:163132/1‑147 (MQ=255)
tCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGaa > 4:197282/1‑149 (MQ=255)
ggCGGGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGcc < 6:130588/148‑1 (MQ=255)
gTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCGGc > 4:341708/1‑148 (MQ=255)
|
ATGAACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGA‑GGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTGGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCGGC > NC_002947_CJ‑RC/1403449‑1403737
|
| 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
