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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
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%
| 46.7
/ NA
| 15 | I106V (ATT→GTT) | ynjI | DUF1266 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/7); total (8/7) |
CAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838735‑1838896
|
cAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCt < 1:160325/90‑1 (MQ=255)
aGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTg < 1:162380/90‑1 (MQ=255)
tAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCttttttt < 2:119810/90‑1 (MQ=255)
ggTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCt > 1:130082/1‑90 (MQ=255)
aTTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCgg > 2:351322/1‑90 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACa > 1:215436/1‑90 (MQ=255)
gcCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACa > 2:195830/1‑90 (MQ=255)
cTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAAt > 2:60463/1‑90 (MQ=255)
gTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATaa < 2:234327/90‑1 (MQ=255)
aCTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGcc < 1:55910/90‑1 (MQ=255)
cTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGccc < 1:51820/90‑1 (MQ=255)
cTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGccc < 2:51297/90‑1 (MQ=255)
tctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCca > 2:172468/1‑90 (MQ=255)
ctcGATACTAAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCcat > 2:173928/1‑90 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTTCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 1:97141/1‑90 (MQ=255)
|
CAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838735‑1838896
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
GGCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGA > NZ_CP009273/1838716‑1838906
|
GGCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACAC < SRR3722116.175179/100‑1 (MQ=60)
AGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAGTCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTT < SRR3722116.304340/100‑1 (MQ=60)
ACTCCAGCGTTTCAGACCATTCCTTATGATAGAACCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGC < SRR3722116.217665/100‑1 (MQ=60)
CAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATG < SRR3722116.162148/100‑1 (MQ=60)
AGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGC < SRR3722116.164232/100‑1 (MQ=60)
GAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCT > SRR3722116.131619/1‑100 (MQ=60)
CAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACA > SRR3722116.218227/1‑100 (MQ=60)
ACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAAT < SRR3722116.56601/100‑1 (MQ=60)
CTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATT < SRR3722116.52459/100‑1 (MQ=60)
ATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTTCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > SRR3722116.98331/1‑100 (MQ=60)
GCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGA > SRR3722116.79419/1‑100 (MQ=60)
|
GGCCAGAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGATAAAGAAAAGA > NZ_CP009273/1838716‑1838906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
