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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 92.9%
| 35.4
/ ‑3.6
| 14 | I106V (ATT→GTT) | ynjI | DUF1266 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (10/3); total (11/3) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.60e-01 |
CGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838730‑1838896
|
cGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCttt < 1:416062/90‑1 (MQ=255)
gTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTa > 1:371583/1‑90 (MQ=255)
gTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTa < 2:200968/90‑1 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 1:160004/1‑90 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 1:228710/1‑90 (MQ=255)
gAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTc > 2:494151/1‑90 (MQ=255)
gATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCttttt > 1:608303/1‑90 (MQ=255)
aaTTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCg > 1:286733/1‑90 (MQ=255)
ttGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGc > 1:462391/1‑90 (MQ=255)
aGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa > 1:206647/1‑90 (MQ=255)
tctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa < 1:557361/77‑1 (MQ=255)
tctcGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGa > 2:557361/1‑77 (MQ=255)
gAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCAtaattaa > 2:342204/1‑90 (MQ=255)
gCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAt > 1:614047/1‑90 (MQ=255)
|
CGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838730‑1838896
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838721‑1838896
|
GAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTA > SRR3722112.376387/1‑100 (MQ=60)
accaccgagatctacacattgacattcgtcggcagcgtcagatgtgtataagagacagGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCC < SRR3722112.301095/42‑1 (MQ=60)
CTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCC < SRR3722112.177606/100‑1 (MQ=60)
CTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCC < SRR3722112.256918/100‑1 (MQ=60)
CGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAA < SRR3722112.421555/100‑1 (MQ=60)
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTC > SRR3722112.161969/1‑100 (MQ=60)
GCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTC > SRR3722112.231459/1‑100 (MQ=60)
TGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTT > SRR3722112.617641/1‑100 (MQ=60)
AGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCG > SRR3722112.290064/1‑100 (MQ=60)
GTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGC > SRR3722112.468940/1‑100 (MQ=60)
GATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGA > SRR3722112.209148/1‑100 (MQ=60)
CAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtaga > SRR3722112.610717/1‑52 (MQ=60)
cagGCCTGTAACTTCTCGATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCC < SRR3722112.565807/97‑1 (MQ=60)
ATACTGAGCGGCTCAACACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > SRR3722112.623487/1‑100 (MQ=60)
|
GAACTCCAGCGTTTCAGACCATTGCTTATGATAGAATCGATAAGGTGCGATCAATTGTAGCGCCTGTAACTTCTCGATACTGAGCGGCTCAATACCTTTAGCCTGATAATAATGCAGTTGTTCTTTTTTTGCTTTAAAACCGGCCCGAACAATAAGCCCCATCATAATTAATAGAT > NZ_CP009273/1838721‑1838896
|
| 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: ‑ |
