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 |
1,782,276 |
T→G |
V192G (GTG→GGG) |
ppsR → |
posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,782,276 | 0 | T | G | 100.0%
| 17.5
/ NA
| 7 | V192G (GTG→GGG) | ppsR | posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (5/2); total (5/2) |
AGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > NZ_CP009273/1782200‑1782358
|
aGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCg > 1:299950/1‑90 (MQ=255)
ggCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCt > 1:53373/1‑90 (MQ=255)
gCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCa < 1:50256/90‑1 (MQ=255)
gTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGt > 2:199616/1‑90 (MQ=255)
tttATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGaa < 2:6665/90‑1 (MQ=255)
gacgaTATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTggcg > 1:236167/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 1:186929/1‑90 (MQ=255)
|
AGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > NZ_CP009273/1782200‑1782358
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ 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
AACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > NZ_CP009273/1782190‑1782358
|
AACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCG > SRR3722091.305045/1‑100 (MQ=60)
GTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCT > SRR3722091.54171/1‑100 (MQ=60)
GCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTC < SRR3722091.50986/100‑1 (MQ=60)
CTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCG > SRR3722091.239802/1‑100 (MQ=60)
GGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > SRR3722091.189664/1‑100 (MQ=60)
|
AACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > NZ_CP009273/1782190‑1782358
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
