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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
886,189 |
A→G |
G7G (GGT→GGC) |
grxA ← |
glutaredoxin 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 886,189 | 0 | A | G | 100.0%
| 64.8
/ NA
| 19 | G7G (GGT→GGC) | grxA | glutaredoxin 1 |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/10); total (9/10) |
GATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCA > NZ_CP009273/886110‑886246
|
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 1:161107/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 2:428692/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 2:366651/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa < 2:161107/90‑1 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa < 1:366651/90‑1 (MQ=255)
tgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGtt < 2:139668/90‑1 (MQ=255)
cTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATa < 2:459152/90‑1 (MQ=255)
tcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCa < 1:689539/48‑1 (MQ=255)
tcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCa > 2:689539/1‑48 (MQ=255)
tcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGc > 2:250131/1‑90 (MQ=255)
tcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGc > 2:478550/1‑90 (MQ=255)
aGATCTTTTGCACACACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATa > 2:152085/1‑75 (MQ=255)
aGATCTTTTGCACACACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATa < 1:152085/75‑1 (MQ=255)
ttttGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATc < 1:400543/90‑1 (MQ=255)
tttGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCa < 2:655750/90‑1 (MQ=255)
acgcacACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGc < 1:58003/46‑1 (MQ=255)
acgcacACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGc > 2:58003/1‑46 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTtctc > 1:709268/1‑39 (MQ=39)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTtctc < 2:709268/39‑1 (MQ=39)
|
GATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCA > NZ_CP009273/886110‑886246
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > NZ_CP009273/886100‑886268
|
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAA > SRR3722073.164352/1‑100 (MQ=60)
cgtcggcagcgtcagatgtgtataagagacagGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGG < SRR3722073.703584/68‑1 (MQ=60)
GATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCAT < SRR3722073.374433/100‑1 (MQ=60)
atcgtcggcagcgtcagatgtgtataagagacagGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTC < SRR3722073.59375/66‑1 (MQ=60)
gacagTTTCTCAGCCAGATCTTTTGCACACACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCC < SRR3722073.155187/95‑1 (MQ=60)
TTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAAT < SRR3722073.409075/100‑1 (MQ=60)
CAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGActgtctcttatacacatctgacgctgccgacgatatgcagt > SRR3722073.723606/1‑59 (MQ=60)
|
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAA > NZ_CP009273/886100‑886268
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
