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 F28 I1 R1
|
155 |
60.3 |
2039550 |
99.3% |
2025273 |
138.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,635,032 |
G→A |
G272G (GGC→GGT) |
ydfN ← |
Qin prophage; putative side tail fiber assembly protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,635,032 | 0 | G | A | 97.4%
| 82.2
/ ‑4.3
| 38 | G272G (GGC→GGT) | ydfN | Qin prophage; putative side tail fiber assembly protein |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (18/19); total (18/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 |
CGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTAT > NC_000913/1634956‑1635165
|
cGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCt > 2:769956/1‑140 (MQ=11)
ggTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTg < 2:295899/140‑1 (MQ=11)
gATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCAt > 2:818618/1‑140 (MQ=11)
gATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCAt > 2:600061/1‑140 (MQ=11)
tgtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt < 2:400478/140‑1 (MQ=14)
tgtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt < 1:708586/140‑1 (MQ=14)
tgtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt < 1:704639/140‑1 (MQ=14)
tCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCt > 2:11384/1‑140 (MQ=14)
tgtgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGc < 1:521783/140‑1 (MQ=14)
tgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTc < 1:358369/133‑1 (MQ=14)
tgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTc > 2:358369/1‑133 (MQ=14)
tgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCAc > 2:717774/1‑140 (MQ=17)
gAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt < 1:11384/140‑1 (MQ=17)
aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTg > 2:961606/1‑135 (MQ=14)
aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTg < 1:961606/135‑1 (MQ=14)
aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGATTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTa > 1:989549/1‑140 (MQ=17)
ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt < 2:516998/137‑1 (MQ=17)
ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt > 1:516998/1‑137 (MQ=17)
ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAcc > 2:68662/1‑140 (MQ=17)
aaTCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGc > 1:162634/1‑140 (MQ=17)
aTCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt > 1:662448/1‑125 (MQ=14)
aTCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt < 2:662448/125‑1 (MQ=14)
aaCGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg < 1:543662/140‑1 (MQ=18)
cGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTtgtg < 1:717774/140‑1 (MQ=18)
aGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCGTTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCcg > 1:470069/1‑140 (MQ=21)
aGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCcg > 1:17751/1‑140 (MQ=21)
ccAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCt > 2:547129/1‑140 (MQ=25)
cAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCtt > 2:192916/1‑140 (MQ=25)
gACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCgcgc < 2:313785/131‑1 (MQ=25)
gACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCgcgc > 1:313785/1‑131 (MQ=21)
gTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAAt < 1:145798/140‑1 (MQ=37)
tATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc > 1:436117/1‑140 (MQ=37)
tATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc < 1:192916/140‑1 (MQ=37)
aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg < 1:592490/140‑1 (MQ=37)
aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg < 2:17751/140‑1 (MQ=37)
aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg < 1:847910/140‑1 (MQ=37)
aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg < 1:818618/140‑1 (MQ=37)
aTGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat < 1:1001846/140‑1 (MQ=255)
|
CGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTAT > NC_000913/1634956‑1635165
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
