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 |
2,003,480 |
T→C |
F60S (TTC→TCC) |
yedK → |
SOS response‑associated peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,003,480 | 0 | T | C | 100.0%
| 33.6
/ NA
| 12 | F60S (TTC→TCC) | yedK | SOS response‑associated peptidase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/4); total (8/4) |
CATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003397‑2003566
|
cATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTgggg > 1:271231/1‑90 (MQ=255)
cATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTgggg > 2:226407/1‑90 (MQ=255)
tGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGata < 2:347195/90‑1 (MQ=255)
cAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGc < 2:76813/90‑1 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 1:97736/1‑90 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 2:318178/1‑90 (MQ=255)
cgcgCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAtggtg > 2:456344/1‑90 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:318178/90‑1 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgcg > 1:330852/1‑90 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgcg > 2:332040/1‑90 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGc > 1:552711/1‑90 (MQ=255)
tGGATCCGGTTTCCTGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTa < 1:555124/90‑1 (MQ=255)
tttcCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAc < 2:290343/90‑1 (MQ=255)
|
CATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003397‑2003566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ 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
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCG > NZ_CP009273/2003387‑2003568
|
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGG > SRR3722111.274552/1‑100 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT > SRR3722111.98947/1‑100 (MQ=60)
CTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCG > SRR3722111.335286/1‑100 (MQ=60)
TCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCGGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722111.322384/100‑1 (MQ=60)
GTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGC > SRR3722111.561395/1‑100 (MQ=60)
TGGATCCGGTTTCCTGGGGATATGCCCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACC < SRR3722111.563857/100‑1 (MQ=60)
GGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCG > SRR3722111.505636/1‑100 (MQ=60)
|
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCG > NZ_CP009273/2003387‑2003568
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
