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 |
|
A10 F1 I2 R1
|
757 |
38.1 |
1607544 |
96.5% |
1551279 |
117.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,432,994 |
(C)6→7 |
coding (567/1125 nt) |
smf ← |
DNA recombination‑mediator A family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,432,988 | 1 | . | C | 97.4%
| 129.8
/ ‑3.3
| 38 | coding (573/1125 nt) | smf | DNA recombination‑mediator A family protein |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (20/17); total (20/18) |
| Fisher's exact test for biased strand distribution p-value = 4.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
TGCTGTCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑G‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACACCATCG > NC_000913/3432850‑3433117
|
tGCTGTCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAgc‑g > 1:13421/1‑139 (MQ=255)
tCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑G‑ccccc < 1:119217/139‑1 (MQ=255)
aaGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGACAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAg < 1:250501/139‑1 (MQ=255)
aGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGACAGc > 2:38461/1‑139 (MQ=255)
caccaccaGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGc < 1:536310/139‑1 (MQ=255)
caGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcg > 2:66318/1‑139 (MQ=255)
aGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcgg < 1:597709/139‑1 (MQ=255)
tACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggcg < 1:66318/139‑1 (MQ=255)
tACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggcg > 2:209215/1‑139 (MQ=255)
cTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGAt > 2:380437/1‑139 (MQ=255)
ttACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGCAC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAAGGCgggtagga < 1:466043/139‑6 (MQ=255)
ttACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGa > 2:30821/1‑139 (MQ=255)
ttACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGa > 1:677363/1‑139 (MQ=255)
tACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa > 2:458712/1‑139 (MQ=255)
aCTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAAt < 2:677363/139‑1 (MQ=255)
tAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGt > 2:146237/1‑139 (MQ=255)
aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCa > 2:77338/1‑96 (MQ=255)
aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCa < 1:77338/96‑1 (MQ=255)
cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAA‑GGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc > 1:428291/1‑139 (MQ=255)
gATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTcc > 2:554728/1‑139 (MQ=255)
aTAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa < 1:30821/139‑1 (MQ=255)
gCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTccc < 2:353877/139‑1 (MQ=255)
cGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑G‑cccccc > 1:611171/1‑63 (MQ=255)
cGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑G‑cccccc < 2:611171/63‑1 (MQ=255)
aaTTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGa < 2:324499/139‑1 (MQ=255)
aTTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGAc > 2:199211/1‑139 (MQ=255)
ttGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACg < 2:13421/139‑1 (MQ=255)
tGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGc < 1:205287/139‑1 (MQ=255)
ggggTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCt > 2:308255/1‑139 (MQ=255)
gggTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTAGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTg > 1:551958/1‑139 (MQ=255)
gTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTa < 1:380437/139‑1 (MQ=255)
gTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATCGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTa > 1:124983/1‑139 (MQ=255)
gAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAgg < 2:390091/139‑1 (MQ=255)
gAACATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAgg > 1:548206/1‑139 (MQ=255)
aaCATCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGgc < 1:209215/139‑1 (MQ=255)
aTCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc < 2:761283/93‑1 (MQ=255)
aTCGAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc > 1:761283/1‑93 (MQ=255)
gAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCAt < 1:691417/63‑1 (MQ=255)
gAGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCAt > 2:691417/1‑63 (MQ=255)
aGGGGAAATTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTa > 2:220372/1‑139 (MQ=255)
aaTTCCGAGACGAGAGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCt < 2:548206/139‑1 (MQ=255)
acgagaGC‑GCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACACCATCg > 2:226095/1‑139 (MQ=255)
|
TGCTGTCACCAGCGAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGC‑G‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACACCATCG > NC_000913/3432850‑3433117
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
