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 |
|
A1 F14 I0 R1
|
248 |
61.6 |
2601574 |
98.7% |
2567753 |
146.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,740,948 |
T→A |
20.3% |
intergenic (+78/+675) |
gltA → / ← yeiW |
citrate synthase/putative oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,740,948 | 0 | T | A | 20.3%
| 31.6
/ 3.8
| 20 | intergenic (+78/+675) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (5/10); new base A (2/2); total (8/12) |
| Fisher's exact test for biased strand distribution p-value = 6.03e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01 |
GGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCACC > NC_002947_CJ‑RC/4740802‑4741096
|
ggCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGc < 3:127569/149‑1 (MQ=255)
cGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCcg < 8:239801/149‑1 (MQ=255)
gTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCcgc < 7:289168/149‑1 (MQ=255)
cgcgCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGa < 5:257935/148‑1 (MQ=255)
cgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAaga < 1:274192/149‑1 (MQ=255)
gcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag < 3:148827/149‑1 (MQ=38)
gcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag < 8:114179/149‑1 (MQ=38)
gcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAagag < 8:140720/149‑1 (MQ=255)
ccAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAgg < 2:187000/149‑1 (MQ=255)
cTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCACATAGCCGCCTTTCCCGCGAAGAGGCCGGCCCAGACACCACAAAACCAAAGTTTTTATACGCCCGCTAACCCACCCCATTGA‑gg > 8:273121/1‑149 (MQ=255)
aagaagGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCACATAGCGGCCGTTCCCGCGAAGAGGCCCGCCCCGACCCCACCAAAAACCACTTTTTGTGCGCCCCCGCACCCACCCCGATGACGGGTATTAAACgcgccaa > 8:313676/1‑143 (MQ=255)
gCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTg > 2:106505/1‑149 (MQ=255)
cgatctCGCGGCCTTGCCCGCGAAGAGGCCTGCACAGACACCACAAAACCTCTGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTg < 1:214587/143‑1 (MQ=255)
cgatctCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTg < 1:214585/143‑1 (MQ=255)
ccTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTgg > 2:110344/1‑149 (MQ=255)
tctTCGCGGGCAAGGCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCt > 1:30030/1‑149 (MQ=255)
tctTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACAACGAACTAGTTGGCCACCATCGCCCGCa > 4:172309/1‑134 (MQ=255)
cgcgGCGTTGCCCGCCATGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGgt < 8:114435/149‑1 (MQ=255)
gcgGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGgtg > 8:197151/1‑149 (MQ=255)
gcgGCCATGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTGACCCCCCGCAAACGCAGCCCGTTCA‑GGGGAATGAAACGCGCAACCACCACCAACGTGTTGGCCAACAAAGCCCGCACGCAACCCCCTg > 2:214585/1‑141 (MQ=255)
ttGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCAcc > 5:292268/1‑149 (MQ=255)
|
GGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCA‑GGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCACC > NC_002947_CJ‑RC/4740802‑4741096
|
| 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
