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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
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%
| 40.5
/ NA
| 14 | D309G (GAT→GGT) | manX | PTS mannose transporter subunit IIAB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/8); total (6/8) |
ATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCA > NZ_CP009273/1897155‑1897299
|
atgaAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGaaaa > 1:35887/1‑90 (MQ=255)
aaaaGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat < 1:383834/90‑1 (MQ=255)
gTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCaa < 2:10822/90‑1 (MQ=255)
gAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGa < 1:258678/90‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa < 2:390974/90‑1 (MQ=255)
tGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGt > 1:255449/1‑90 (MQ=255)
aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa < 2:255449/90‑1 (MQ=255)
gTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTgtgt < 1:85799/90‑1 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:358244/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:416400/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:58556/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 2:386980/1‑90 (MQ=255)
aGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCa < 1:151759/90‑1 (MQ=255)
aGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCa < 2:408578/90‑1 (MQ=255)
|
ATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCA > NZ_CP009273/1897155‑1897299
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
GTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTA > NZ_CP009273/1897145‑1897319
|
GTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAA > SRR3722113.36191/1‑100 (MQ=60)
AAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATC < SRR3722113.387846/100‑1 (MQ=60)
TTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGT > SRR3722113.257681/1‑100 (MQ=60)
GAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGT < SRR3722113.260945/100‑1 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722113.361917/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722113.420795/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722113.59062/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC < SRR3722113.86559/100‑1 (MQ=60)
AGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACAC < SRR3722113.153020/100‑1 (MQ=60)
GTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTA > SRR3722113.383406/1‑100 (MQ=60)
|
GTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCTTA > NZ_CP009273/1897145‑1897319
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
