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 |
|
A11 F1 I1 R1
|
757 |
76.1 |
3598070 |
93.4% |
3360597 |
108.6 |
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 | 90.4%
| 160.1
/ 8.4
| 52 | 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 . (4/1); new base C (20/27); total (24/28) |
| Fisher's exact test for biased strand distribution p-value = 1.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAA > NC_000913/2767305‑2767568
|
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ccc‑cc > 2:1690626/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ccc‑cc > 1:1341166/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑caacc > 2:1326195/1‑135 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ctcaca > 2:839399/1‑134 (MQ=255)
ttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ccc‑ccc‑cctca < 1:886362/139‑5 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑caca < 2:1341166/139‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCCTTCTAAACGAACCAGTATAGAATCCGCCCTTTTGGCATGCTATTAACTTGCCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑caca < 2:1141065/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTc < 2:449631/139‑1 (MQ=255)
cGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCC‑CCC‑CT‑‑CACAACGTCCt > 1:660878/1‑139 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAggg > 2:1185531/1‑139 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAggg < 2:1771511/139‑1 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCC‑CCC‑CT‑‑CACAACGTCCTGCAAAGGGAac < 2:660878/139‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAac > 1:852370/1‑135 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAac < 2:852370/135‑1 (MQ=255)
ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑caca < 2:331790/115‑1 (MQ=255)
ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑caca > 1:331790/1‑115 (MQ=255)
cTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGtttt < 1:310649/139‑1 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTccc < 1:1690626/139‑1 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTccc < 1:1185531/139‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑CCC‑CCC‑CT‑‑CACAACGTCCTGAATAGGGAACACGCTTTCCCCtata > 1:358263/1‑136 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGtt < 1:1556177/129‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGtt > 2:1556177/1‑129 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg > 2:1134128/1‑139 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGGCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAccc < 1:1134128/139‑1 (MQ=255)
tcttctTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CTCACACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt < 1:73396/139‑1 (MQ=255)
tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:1326195/139‑1 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTc > 1:425546/1‑88 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTc < 2:425546/88‑1 (MQ=255)
aCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCC‑CCCTCT‑‑CACAACATCCTACATAGCGACCACATATGACACTGTGCACCCACGACTACATTTcccacaca > 2:790449/1‑134 (MQ=255)
aaCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa < 1:839399/139‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTccc > 2:982277/1‑105 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTccc < 1:982277/105‑1 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACAAGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCaat > 1:1149142/1‑139 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ccc‑c > 1:896646/1‑58 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ccc‑c < 2:896646/58‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCtgt < 1:1579542/94‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCtgt > 2:1579542/1‑94 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGa > 1:1164757/1‑104 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGa < 2:1164757/104‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTTAATAATGt > 1:1521809/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCCACCC‑CT‑‑CACAACGTCCCGCATAGGGAACAAGTTTTCGCCTGCGCACCCCCGACTAAATTTTCCCCCCTTAACACTACCCaaaaatct > 1:599/1‑137 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACCACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:599/139‑1 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATATGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGACACCAATTTTCTGGAAATCCTatg > 2:114412/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCa > 2:326181/1‑76 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCa < 1:326181/76‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa > 1:807842/1‑98 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa < 2:807842/98‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga > 1:46295/1‑139 (MQ=255)
tatGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CCCAACGTCCTCCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa > 2:1392651/1‑95 (MQ=255)
tatGATCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa < 1:1392651/95‑1 (MQ=255)
aTCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAac > 2:604199/1‑46 (MQ=255)
aTCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAac < 1:604199/46‑1 (MQ=255)
tCAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTCACCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTTTCGAAATCCTATGATGCCTTTccc > 2:1671390/1‑139 (MQ=255)
cAAATAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg < 1:790449/139‑1 (MQ=255)
tAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGtttt > 2:1037398/1‑47 (MQ=255)
tAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGtttt < 1:1037398/47‑1 (MQ=255)
tAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg > 1:163909/1‑55 (MQ=255)
tAGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg < 2:163909/55‑1 (MQ=255)
aGCATT‑AACCCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTTAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaaa < 2:1521809/139‑1 (MQ=255)
|
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCC‑CCC‑CT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAA > NC_000913/2767305‑2767568
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
