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 |
|
A5 F13 I0 R1
|
213 |
60.4 |
2554362 |
98.6% |
2518600 |
147.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,463 |
T→A |
20.7% |
intergenic (‑124/+47) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,463 | 0 | T | A | 20.7%
| 52.3
/ 8.6
| 29 | intergenic (‑124/+47) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base T (11/12); new base A (2/4); total (13/16) |
| Fisher's exact test for biased strand distribution p-value = 6.63e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATCACCACCTCAGCCGAGCGTT > NC_002947_CJ‑RC/5558323‑5558610
|
cgggcgtacatgagcaactccttttgtcatgtgtcgccgacagcaaagcaacaccgctccggtgtgggagcggccttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCa < 7:228199‑M2/45‑1 (MQ=255)
gggcggacatgagcaactccttttgtcatgtgtcgccgacagcatagcaacaccgctcaggtgtgggagcggccttgtgtcgcgaaagggccgcattgcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAg < 8:310724‑M2/46‑1 (MQ=255)
gggggacatgagcaactccttttggcatgtgccgccgacagaataccaacaccgctctgttgtgggcgcggccgtgtgtcgctaacggcccgcatcgcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGc < 1:25510‑M2/47‑1 (MQ=255)
ggCGCACATTACAAACTCTTTTTGTCTTGTGGCCCCTACAGCATACCAACCCCGCTCTGGTGTGGGCGGGGCCTTGTGCCGCTAACGGCCCGAATCGCGGCCCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGc < 2:149332/149‑1 (MQ=255)
gcaactccttttgtcatgtgtcgccgacagaatagcaacacctctcaggtgtgggtgcggccttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 8:13187‑M2/57‑1 (MQ=255)
tccttttgtcatgtgtcgccgacagcatagcaacaccgctcaggtgtgggagcggccttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCATAGCagcccca < 1:32158‑M2/51‑3 (MQ=255)
tccttttgtcatgtgtcgccgacagcatagcaacaccgctcaggtgtgggagcggccttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCATAGCagcccca > 2:32158‑M2/87‑135 (MQ=255)
gtgtcgccgacagaatagaaacaccgctctggtgtgggcggggccttgtgtcgctaacgggccgaataggggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCACGACACAAGGCCCACAAAg < 8:197366‑M2/73‑1 (MQ=255)
accgctcaggtgtgggagcggccttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCATAGCagcccca > 8:2510‑M2/53‑101 (MQ=255)
accgctcaggtgtgggagcggccttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCATAGCagcccca < 7:2510‑M2/51‑3 (MQ=255)
ttgtgtcgcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 6:111275‑M2/30‑149 (MQ=255)
gcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 1:28446‑M2/23‑149 (MQ=255)
gcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 6:267518‑M2/23‑149 (MQ=255)
gcgaaagggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 6:20136‑M2/23‑149 (MQ=255)
agggccgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGCCCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:75737‑M2/18‑145 (MQ=255)
cgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGc < 1:221686‑M2/109‑1 (MQ=255)
cgcatagcggccCCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGc > 2:221686‑M2/13‑121 (MQ=255)
ccGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAACGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCAGGCGCGCAGCTGAGCCGCCAGATCATCCAGCAccaagc > 2:147600/1‑144 (MQ=255)
cGGCAATTTCCGCG‑TGTATCCAACAACCCTGGGGCGGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTa < 8:1683/149‑1 (MQ=255)
gcaaaTTCCCGCG‑TTAATCCAACAACCGGGGGGCTGATATGCCGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTAc < 7:297253/146‑1 (MQ=255)
gCAATTTCCGGGTTTTATCAAACAACCGTGGGGCTCTAATCCCCCCCTTGCCCCACCAAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTAc < 3:158880/149‑1 (MQ=255)
tCCGCG‑TTTATGCAAAAAACCTGGGGCTGCTATGCAGCCCTTTCGCTAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCg < 4:269256/148‑1 (MQ=255)
gcg‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGt > 1:239650/1‑149 (MQ=255)
cg‑TGTATGCAACAACCCTGGGGCTGCTTTGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTc < 4:254898/149‑1 (MQ=255)
aTGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCAt > 1:62742/1‑149 (MQ=255)
aacaaACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATcac > 4:111216/1‑148 (MQ=255)
aaacccgggggCTGCAATGCAGCCCTTTCGCCAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATcaccac < 4:19645/142‑1 (MQ=255)
aCCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATCACCACCt > 7:14275/1‑148 (MQ=255)
ggggCTGATATGCTCCCCTTTGGCGAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATCACCACCTCAGcc < 6:206947/149‑1 (MQ=255)
gctATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATCACCACCTCAGCCGAGCGt > 6:285898/1‑149 (MQ=255)
ttATCCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATCACCACCTCAGCCGAGCGtt < 7:3786/148‑1 (MQ=255)
|
CGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCG‑TGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGATCATCCAGCACCTTGCTACTGGCCGTGGTCTGCATCACCACCTCAGCCGAGCGTT > NC_002947_CJ‑RC/5558323‑5558610
|
| 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
