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 |
|
A2 F9 I0 R1
|
142 |
103.7 |
2603848 |
81.8% |
2129947 |
227.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
766,690 |
T→C |
31.6% |
L236P (CTC→CCC) |
mngA → |
fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 766,690 | 0 | T | C | 31.6%
| 11.3
/ 2.5
| 16 | L236P (CTC→CCC) | mngA | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| Reads supporting (aligned to +/- strand): ref base T (8/2); new base C (2/2); total (10/6) |
| Fisher's exact test for biased strand distribution p-value = 5.20e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.96e-01 |
GGCGACGACGCCTGATGAGTTGCTCTCGGCGCTGGATGACAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCAATAGTG‑CAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGA > NC_000913/766454‑766922
|
ggCGACGACGCCTGATGAGTTGCTCTCGGCGCTGGATGACAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGGTTAA‑C‑GGCGTGTCCACTCa > 2:753638/1‑239 (MQ=255)
cgCCTGATGAGTTGCTCTCGGCGCTGGATGACAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGGCGCAAACTCGGCGTAAATGTTTCCGTTGAAAAACAAGGCGGTAACGGCCTTGAAGGGCGGTTAA‑C‑GGCGGGTCAACCCacaaaggcc > 2:1082174/1‑231 (MQ=255)
cgCCTGATGAGTTGCTCTCGGCGCTGGATGACAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGCCGCAAACTCGGCGTAAATTTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCCAAAGtac > 2:1212609/1‑236 (MQ=255)
ctctCGGCGCTGGATGACAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTTAAGGGCGTTTAA‑C‑GGCGGATCCAATCCAAAGTG‑CAACccccctcatttt > 2:684075/1‑231 (MQ=255)
cAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAAAAAGGCGCTAACGGCCTTGAAGGGGTTTTAA‑C‑GACGGAGGACACCAATAAGG‑CAAACGCCTGGCATTTTTCGGCTGAAATCGccc > 2:541489/1‑238 (MQ=255)
tGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCaa < 1:1046382/137‑1 (MQ=255)
ctaatagGGCTGTGAAATATAAGGAAAACGCCGGCCAAAACCTGGGAAAAATTTTTTAGGTTAAAAAACAGGGC‑ATGAGGGGATTGAAGGGGTTTTAAGC‑GGGGAATCACCACAATAGGC‑AAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCcaa < 2:1230660/236‑1 (MQ=255)
tatGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCAATAGTG‑CAACCGCCTGTATTTTTTCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGGTTTAAATGCATTCCCCCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCCTGCAGAAGCGTTGATCcaacaa > 2:359102/1‑238 (MQ=255)
cTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCAATAGTG‑CAACCGCCTGTATTTTTTCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCCCGCTTTCAGTGCCTGTTGCCGAGCCGCTTCGCCATGCAGAAGCGTTGTTccccgtctctttt > 2:847627/1‑228 (MQ=255)
cTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCAATAGTG‑CAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGGTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTTCCGAGCCGATTCGCCATGCCGAAGCGTTGATCCAACAAacgcct > 2:388590/1‑237 (MQ=255)
acgcgggagcaaaaCTGGGCATAATTTTTCAGGTTAAAAAACAGGGC‑CTAAACGATATGGAGGGGTTTTAA‑CGGGCGGACCAACCAAATAGTG‑CAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGAt < 2:116302/228‑1 (MQ=255)
gCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCAATAGTG‑CAACCGCCTGTATTTTTTCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGGATTTCCCCGCTTTCAGTGCCCGTTTCCGGGCCGGTTCGCCCTGCAGAAACGTTGATCCAACAAacg > 2:813219/1‑216 (MQ=255)
aaaccggggataaattttttACGTAAAAAAACAGGGCG‑TAACGGGATTGAAGGGGTTTTAA‑A‑GGGGGATAAACCAAAAGGGGACACCCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGcgta < 2:988212/222‑1 (MQ=255)
tgttacggggaggATCCACAAAATTGTG‑CAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAgg < 2:397861/227‑1 (MQ=255)
cggATCAACTCAATAGTG‑CAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGGGTCAAAAAGGGGCTGAAACacaggctcttatac > 2:983702/1‑226 (MQ=255)
acAACTAAATGGGG‑CACCCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGa < 2:1179199/237‑1 (MQ=255)
|
GGCGACGACGCCTGATGAGTTGCTCTCGGCGCTGGATGACAAGGGAGGCACGCAACCTTCTGCCTCTTTTTCCAACGCGCCAACTATCGTCTGCGTAACGGCCTGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTACGTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAA‑C‑GGCGGATCAACTCAATAGTG‑CAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGA > NC_000913/766454‑766922
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
