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 |
|
A1 F2 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,671,899 |
T→G |
T88P (ACG→CCG) |
pntA ← |
Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,671,899 | 0 | T | G | 100.0%
| 64.2
/ NA
| 19 | T88P (ACG→CCG) | pntA | Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (9/10); total (9/10) |
CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTC > NZ_CP009273/1671816‑1671981
|
cATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTccc > 2:70854/1‑90 (MQ=255)
ccATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGAt < 1:70854/90‑1 (MQ=255)
gttCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat > 1:362369/1‑90 (MQ=255)
ccGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCa < 2:28430/90‑1 (MQ=255)
cGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAg > 1:415927/1‑90 (MQ=255)
ggATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGa > 2:181466/1‑90 (MQ=255)
aTTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAAt < 1:545332/90‑1 (MQ=255)
cTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGAt > 2:580402/1‑90 (MQ=255)
gATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAAt > 1:330933/1‑42 (MQ=255)
gATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAAt < 2:330933/42‑1 (MQ=255)
aaaaCTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGAc < 2:47687/90‑1 (MQ=255)
cTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTa > 1:490381/1‑90 (MQ=255)
tCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAt < 1:10130/90‑1 (MQ=255)
tCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTAt < 2:267876/90‑1 (MQ=255)
cACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat > 1:488638/1‑38 (MQ=39)
cACCAGCGGTGTCCCAGGATTCAGTAACGCAATTtcat < 2:488638/38‑1 (MQ=39)
cACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCtt < 2:316456/60‑1 (MQ=255)
cACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCtt > 1:316456/1‑60 (MQ=255)
aCCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTc < 1:580402/90‑1 (MQ=255)
|
CATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTC > NZ_CP009273/1671816‑1671981
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAA > NZ_CP009273/1671810‑1671991
|
agatgtgtataagagacaGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGA < SRR3722073.351602/82‑1 (MQ=60)
CCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGC < SRR3722073.72504/100‑1 (MQ=60)
GTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCAT > SRR3722073.370050/1‑100 (MQ=60)
GCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAG > SRR3722073.424815/1‑100 (MQ=60)
ATTCTGCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGAC < SRR3722073.556714/100‑1 (MQ=60)
GCGCAGGCCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTctgtctcttatacacatctgacgctgccgacgatatgc > SRR3722073.337968/1‑62 (MQ=60)
CCAGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTA > SRR3722073.500774/1‑100 (MQ=60)
AGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCtgtctcttatacacatctgacgctgccgacgatatgcagtg > SRR3722073.499012/1‑59 (MQ=60)
AGATAAAACTCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCctgtctcttatacacatctg > SRR3722073.323161/1‑80 (MQ=60)
TCACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTAC < SRR3722073.10384/100‑1 (MQ=60)
ACCAGCGGTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAA < SRR3722073.592516/100‑1 (MQ=60)
|
AGAGTCCATCGCCATCACGGTCACGTTACGTTCCGCAAGTTTTTGCATTAATTCCGGATTCTGCGCAGGCCAGATAAAACTCACCAGCGTTGTCCCAGGATTCAGTAACGCAATTTCATCATCTAACGGCGCATTGACCTTCAGAATGATCTCTGACTGCCAGACGCTATTCCCTTCTACAA > NZ_CP009273/1671810‑1671991
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
