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 |
|
A6 F1 I2 R1
|
758 |
59.3 |
2864096 |
93.9% |
2689386 |
105.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,767,445 |
(C)7→8 |
intergenic (+90/‑265) |
rnlB → / → yfjP |
CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,767,438 | 1 | . | C | 92.1%
| 115.4
/ 3.0
| 38 | intergenic (+83/‑272) | rnlB/yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base C (15/20); total (17/21) |
| Fisher's exact test for biased strand distribution p-value = 5.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767301‑2767571
|
aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c > 2:1288023/1‑139 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc > 2:623206/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cccc < 1:735163/139‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca < 1:216495/139‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca < 1:1288023/139‑1 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGt < 2:402408/139‑1 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGt < 1:623206/139‑1 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca < 2:577711/123‑1 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca > 1:577711/1‑123 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc < 2:1080056/122‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc > 1:1080056/1‑122 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCCCCC‑CACAACGTCCTGCATAGGGAac < 2:176824/133‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCCCCC‑CACAACGTCCTGCATAGGGAac > 1:176824/1‑133 (MQ=255)
cTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATACAA‑TCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTc < 2:1392680/139‑1 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgt > 1:414294/1‑139 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTACTGCATAGGGAACACGTTTTCCCCtgt > 2:765792/1‑139 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac < 1:1085708/124‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac > 2:1085708/1‑124 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac < 1:1276290/119‑1 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac > 2:1276290/1‑119 (MQ=255)
aaCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGAc < 2:414294/139‑1 (MQ=255)
tctAAACGAATCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:691185/139‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc > 1:1309985/1‑67 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc < 2:1309985/67‑1 (MQ=255)
tttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑CACCCACATCACAAAGTACTACATAGGGAAAACGAATAAACCTGTGGACCAAAGAAAAAATTACCACCCCTTTAAACATataaataaaataaaaa > 1:747518/1‑131 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc < 1:1171919/53‑1 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTc > 2:1171919/1‑53 (MQ=255)
tatTAACTTGTCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGa < 1:720206/139‑1 (MQ=255)
gTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca > 1:590395/1‑38 (MQ=255)
gTCCAATATGATCAAATAGCATTAACC‑CCCCCCTcaca < 2:590395/38‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac > 2:61872/1‑55 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAac < 1:61872/55‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 1:499165/1‑74 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 2:168500/1‑74 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:168500/74‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:499165/74‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt > 2:1315315/1‑81 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt < 1:1315315/81‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc > 2:770659/1‑90 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:770659/90‑1 (MQ=255)
aGCATTACCC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGATTTCCCCTCTGCACCCACGACTAAGTTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCCATGATGCCTTTCCCGGTaaa < 2:890362/139‑1 (MQ=255)
aTTAACC‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTTCACCCACGAATAAATTACCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATgg > 2:1280413/1‑139 (MQ=255)
|
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767301‑2767571
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
