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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,897,230 |
A→G |
D309G (GAT→GGT) |
manX → |
PTS mannose transporter subunit IIAB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,897,230 | 0 | A | G | 100.0%
| 55.6
/ NA
| 18 | D309G (GAT→GGT) | manX | PTS mannose transporter subunit IIAB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/8); total (10/8) |
AAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTC > NZ_CP009273/1897159‑1897316
|
aaaaGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat < 2:16016/90‑1 (MQ=255)
cGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGAt > 2:156691/1‑90 (MQ=255)
cGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCa > 2:80361/1‑90 (MQ=255)
tCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCaaaa > 2:304232/1‑90 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa < 1:243433/90‑1 (MQ=255)
cTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAg < 2:50095/90‑1 (MQ=255)
gAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTa > 1:222323/1‑90 (MQ=255)
aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa < 1:431381/90‑1 (MQ=255)
aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa < 2:134384/90‑1 (MQ=255)
gTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTgtgt < 1:304232/90‑1 (MQ=255)
gTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTgtgt < 1:442479/90‑1 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:239317/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:231727/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 2:30967/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 2:371688/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 2:413612/1‑90 (MQ=255)
tCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTa > 2:170385/1‑90 (MQ=255)
ccGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTc < 2:231727/90‑1 (MQ=255)
|
AAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTC > NZ_CP009273/1897159‑1897316
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTA > NZ_CP009273/1897176‑1897319
|
TCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTA > SRR3722111.225020/1‑100 (MQ=60)
AACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAT < SRR3722111.246321/100‑1 (MQ=60)
AATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGT < SRR3722111.437816/100‑1 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722111.234511/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722111.242161/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC < SRR3722111.308181/100‑1 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC < SRR3722111.449139/100‑1 (MQ=60)
GGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTT > SRR3722111.510100/1‑100 (MQ=60)
GTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGACTTA > SRR3722111.578899/1‑100 (MQ=60)
|
TCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTA > NZ_CP009273/1897176‑1897319
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
