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 |
5,462,375 |
T→G |
43.4% |
intergenic (+18/‑22) |
PP_4795 → / → holA |
lipoprotein/DNA polymerase III subunit delta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,462,375 | 0 | T | G | 43.4%
| 11.1
/ 5.3
| 23 | intergenic (+18/‑22) | PP_4795/holA | lipoprotein/DNA polymerase III subunit delta |
| Reads supporting (aligned to +/- strand): ref base T (3/8); new base G (6/3); total (12/11) |
| Fisher's exact test for biased strand distribution p-value = 1.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCCAACTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGT > NC_002947_CJ‑RC/5462230‑5462522
|
cccAACTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCgg < 1:37761/149‑1 (MQ=255)
cccAACTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCgg < 2:77878/149‑1 (MQ=255)
aCTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCCCCGgcgc > 3:129901/1‑149 (MQ=255)
gATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGGCCCg > 7:22174/1‑149 (MQ=255)
aGCTTAACGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCGGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTcccc < 6:113181/149‑1 (MQ=255)
cccAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGCCCTCGGGCGGCCCGCCGGGTGCCCCGGAAAAACccccccccccca > 3:306080/1‑147 (MQ=255)
cctaaGCTGCCGCGGTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAATTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTcaac < 6:228255/146‑1 (MQ=255)
gAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGGCCGCGGGGGGCCCGCCGGTGGCCCCGGGAACGCGCCCCCGCCCCCCTcaacca > 5:86123/1‑147 (MQ=255)
gCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGCCCGCGGGCGCCCCCCCGGGTGCCCCGGGAACGAGCCCCCCCCCCCCGcaacaaccccca > 5:208146/1‑143 (MQ=255)
cgcgCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGc < 2:45206/149‑1 (MQ=255)
gcTGGTGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGATGTACCGGGAAACAAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAg < 5:229118/149‑1 (MQ=255)
gcTGGCGGCTGCCCGCCGCCAGCAAGCCGACACGCCTCAGCAACCGCCACTGTAATTACCGGCCAACTACGCCCGCGTGGGGCGCCCGGGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAg < 4:198756/149‑1 (MQ=255)
ggCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCACGGGCGCCCCCCCGGTTGCCCATTAAACAAGCCCCCCCCCCACACAAAAACCACCAGCAAGGcccc > 2:239053/1‑148 (MQ=255)
tGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCCCCGGGTGCCCCTGAAACACCCCCCCCCCCCACGCCAAAACCCCCAGCAACGCCCCCggg > 8:34841/1‑149 (MQ=255)
cgccAGCAAGCCTCGACGCCTCACCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGt < 8:133498/149‑1 (MQ=255)
cAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCGCCGCGTGCCCATGTAACTCGCCCCCCCCCCACTCAACCACCCCACGCACGGCGCCCTGGGCCCGGTCTa > 2:147624/1‑149 (MQ=255)
ccTCACCAATCCCCACTGGAAGTACCGGCAAACTAACCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGcga < 4:129901/149‑1 (MQ=255)
gCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCGCCAGTTACCCCAGCAAAAAGCCCCCCCCCCACGCAACAACCACCAGCAACGTGCCCAGGCCCCGGTCTACGAGGTCAGTGGCGCCGccc > 8:87855/1‑149 (MQ=255)
cACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCACCGGCGCCCCCCCGGGTAACCCAAAAACACGCCCCCCCCCCAAAAAACAAACCCCAGCAAACCCCCCAGGCCCCCGGCTAAGTGGGAACTGGGGACGACCCCcagctg > 6:138906/1‑149 (MQ=255)
ggggCGCCGGGGGGCCCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATg < 1:197277/149‑1 (MQ=255)
gcgcCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcg > 3:121825/1‑149 (MQ=255)
cccTCGGGGGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcgcgc < 8:22174/149‑1 (MQ=255)
cTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGt > 4:50608/1‑149 (MQ=255)
|
CCCAACTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGT > NC_002947_CJ‑RC/5462230‑5462522
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
