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 F5 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,041,277 |
T→C |
intergenic (‑18/+28) |
gfcE ← / ← gfcD |
polysaccharide export protein/YjbH domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,041,277 | 0 | T | C | 84.6%
| 26.3
/ 0.4
| 13 | intergenic (‑18/+28) | gfcE/gfcD | polysaccharide export protein/YjbH domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (7/4); total (8/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.04e-01 |
TCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACCG > NZ_CP009273/1041156‑1041411
|
tCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGaa > 2:436913/1‑139 (MQ=255)
ccTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAAt > 2:467329/1‑139 (MQ=255)
aCTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTc < 1:467329/138‑1 (MQ=255)
gTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCaatgtaat > 1:119312/1‑119 (MQ=255)
gTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCaatgtaat < 2:119312/119‑1 (MQ=255)
tCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTg > 2:289418/1‑138 (MQ=255)
gTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGc < 1:208223/126‑1 (MQ=255)
gTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGc > 2:208223/1‑126 (MQ=255)
aaTGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCa < 1:289418/139‑1 (MQ=255)
aTCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCAt > 1:483881/1‑110 (MQ=255)
aTCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCAt < 2:483881/110‑1 (MQ=255)
aTCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAaccacc > 1:68722/1‑139 (MQ=255)
tCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACcg > 1:302851/1‑139 (MQ=255)
|
TCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACCG > NZ_CP009273/1041156‑1041411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATTGTCAGGTAGTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACCGC > NZ_CP009273/1041134‑1041412
|
gaagacggcatacgatatctagtacggtctcgtgggctcggagatgtgtataagagacAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTA < SRR3722132.577921/93‑1 (MQ=60)
CCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACtgtctctt > SRR3722132.121500/1‑142 (MQ=60)
TACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTC < SRR3722132.475702/150‑1 (MQ=60)
cagGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCG < SRR3722132.212118/148‑1 (MQ=60)
AAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGG < SRR3722132.294921/151‑1 (MQ=60)
GGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATctgtctcttatacacatct > SRR3722132.492504/1‑132 (MQ=60)
GGTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACCG > SRR3722132.69970/1‑151 (MQ=60)
GTTTATATTTATCAGCCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACCGC > SRR3722132.308561/1‑151 (MQ=60)
|
ATTGTCAGGTAGTTCAATGACATCCTTGTTACTGGTCGATAAATTCTGACCAGGAACAAGGGTACATGCTGTCAAAGACAGAACAGCCAATGTCAGTACCGAAAACTTAAAAATGTTCTTTTTCATTGGTTTATATTTATCAGTCAATGTAATGTTATGAATTACGTCAGGTTATTGTCCAACCGGTACTTCTCGCTCTGCCGTCATTGGATAGAGCTGGTATTTGCGTGACAGCATTTGTCCACCATCACGCGTCAATGGTGTCCACGAAACCACCGC > NZ_CP009273/1041134‑1041412
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
