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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
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%
| 34.8
/ NA
| 13 | F60S (TTC→TCC) | yedK | SOS response‑associated peptidase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/8); total (5/8) |
ACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTA > NZ_CP009273/2003394‑2003557
|
aCCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACCGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTg < 2:204306/90‑1 (MQ=255)
cATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTgggg > 1:244883/1‑90 (MQ=255)
gATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTc > 2:228778/1‑90 (MQ=255)
tACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTccc > 2:229413/1‑90 (MQ=255)
cAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCgg < 1:115720/90‑1 (MQ=255)
cTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAAc > 1:175261/1‑90 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:132689/90‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:228778/90‑1 (MQ=255)
gAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTa < 1:25977/90‑1 (MQ=255)
cGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGaa > 1:321862/1‑90 (MQ=255)
gTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGaaa < 2:321862/90‑1 (MQ=255)
cTGGATCCGGTTTCCTGGGGATATGCCCCGGGATGGTGGGATAACCCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGt < 1:229413/90‑1 (MQ=255)
tGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTa < 2:246356/90‑1 (MQ=255)
|
ACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTA > NZ_CP009273/2003394‑2003557
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003387‑2003566
|
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGG > SRR3722091.248701/1‑100 (MQ=60)
CAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGAT < SRR3722091.117471/100‑1 (MQ=60)
CAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAAC > SRR3722091.177779/1‑100 (MQ=60)
GCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAA > SRR3722091.327422/1‑100 (MQ=60)
TCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722091.134679/100‑1 (MQ=60)
TAAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722091.232313/100‑1 (MQ=60)
GAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGG < SRR3722091.26340/100‑1 (MQ=60)
CTGGATCCGGTTTCCTGGGGATATGCCCCGGGATGGTGGGATAACCCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC < SRR3722091.232956/100‑1 (MQ=60)
|
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003387‑2003566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
