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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,838,813 |
T→C |
I106V (ATT→GTT) |
ynjI ← |
DUF1266 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,838,813 | 0 | T | C | 100.0%
| 50.7
/ NA
| 17 | I106V (ATT→GTT) | ynjI | DUF1266 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/8); total (9/8) |
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCA > NZ_CP009273/1838744‑1838884
|
gCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATaataat > 2:35032/1‑90 (MQ=255)
tATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCa > 1:129468/1‑90 (MQ=255)
tATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCa > 2:55789/1‑90 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 1:92543/1‑90 (MQ=255)
gATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttt > 1:92612/1‑90 (MQ=255)
ttaaTTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAAc < 2:222366/88‑1 (MQ=255)
gcgcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt < 2:200285/71‑1 (MQ=255)
gcgcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt > 1:200285/1‑71 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACa > 1:312485/1‑90 (MQ=255)
ccTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACaa > 1:120782/1‑90 (MQ=255)
tGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATa < 2:89923/90‑1 (MQ=255)
cTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGccc < 2:129468/90‑1 (MQ=255)
ttCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGcccc < 1:49121/90‑1 (MQ=255)
ctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGcc > 2:159947/1‑73 (MQ=255)
ctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGcc < 1:159947/73‑1 (MQ=255)
cGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcatca < 1:35032/90‑1 (MQ=255)
cGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcatca < 2:28150/90‑1 (MQ=255)
|
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCA > NZ_CP009273/1838744‑1838884
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGA > NZ_CP009273/1838737‑1838906
|
GACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCA > SRR3722076.130989/1‑100 (MQ=60)
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTC > SRR3722076.93674/1‑100 (MQ=60)
TGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTT > SRR3722076.93743/1‑100 (MQ=60)
ATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCtgtctctt > SRR3722076.202842/1‑92 (MQ=60)
CAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACA > SRR3722076.317222/1‑100 (MQ=60)
AATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAA > SRR3722076.122213/1‑100 (MQ=60)
gagacaGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAA < SRR3722076.161870/94‑1 (MQ=60)
TTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTA < SRR3722076.49734/100‑1 (MQ=60)
CGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAG < SRR3722076.35447/100‑1 (MQ=60)
GCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGA > SRR3722076.76379/1‑100 (MQ=60)
|
GACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGA > NZ_CP009273/1838737‑1838906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
