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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,536,106 |
T→C |
E261G (GAA→GGA) |
cysP ← |
thiosulfate/sulfate ABC transporter substrate‑binding protein CysP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,536,106 | 0 | T | C | 96.4%
| 81.9
/ ‑3.4
| 28 | E261G (GAA→GGA) | cysP | thiosulfate/sulfate ABC transporter substrate‑binding protein CysP |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (19/8); total (20/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
TATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAA > NZ_CP009273/2536023‑2536191
|
tATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTAc > 2:213637/1‑90 (MQ=255)
tATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTAc > 2:451119/1‑90 (MQ=255)
tCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGt < 1:183551/90‑1 (MQ=255)
gcgGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGc > 1:361129/1‑90 (MQ=255)
agtaATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCa < 1:451119/90‑1 (MQ=255)
aGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGtttt > 1:286620/1‑90 (MQ=255)
aGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGtttt > 1:365664/1‑90 (MQ=255)
aGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGttt > 2:137298/1‑89 (MQ=255)
aGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGttt < 1:137298/89‑1 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 1:263409/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 2:496234/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 2:34727/1‑90 (MQ=255)
gTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGt < 2:64647/65‑1 (MQ=255)
gTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGt > 1:64647/1‑65 (MQ=255)
ggTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGc < 1:12467/90‑1 (MQ=255)
ggTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGc > 1:322202/1‑90 (MQ=255)
gcgcCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCg > 1:440572/1‑90 (MQ=255)
gCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAAtt > 1:148505/1‑90 (MQ=255)
gCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGt > 2:73534/1‑90 (MQ=255)
gCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGt > 1:184847/1‑90 (MQ=255)
cAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTg > 2:215514/1‑90 (MQ=255)
aGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTgg > 2:217220/1‑90 (MQ=255)
aGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTgg > 1:83271/1‑90 (MQ=255)
gATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCg > 2:206099/1‑90 (MQ=255)
aGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGaa < 2:157795/90‑1 (MQ=255)
ttGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATcacc < 2:365664/90‑1 (MQ=255)
gcTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGcc > 2:313562/1‑60 (MQ=255)
gcTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGcc < 1:313562/60‑1 (MQ=255)
ttttcCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCaaa < 2:440572/90‑1 (MQ=255)
|
TATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAA > NZ_CP009273/2536023‑2536191
|
| 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
GGTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > NZ_CP009273/2536020‑2536203
|
GGTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGC > SRR3722111.366143/1‑100 (MQ=60)
TCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCAC < SRR3722111.185843/100‑1 (MQ=60)
CGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTT > SRR3722111.290263/1‑100 (MQ=60)
CGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTT > SRR3722111.370796/1‑100 (MQ=60)
GTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCtgtctcttatacacatctg > SRR3722111.25717/1‑81 (MQ=60)
GTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTA > SRR3722111.266539/1‑100 (MQ=60)
AGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATC < SRR3722111.457964/100‑1 (MQ=60)
GTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCctgtctcttatacac > SRR3722111.65411/1‑85 (MQ=60)
TAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCC < SRR3722111.139029/100‑1 (MQ=60)
CGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGC > SRR3722111.326480/1‑100 (MQ=60)
ATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCG > SRR3722111.447193/1‑100 (MQ=60)
GGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGctgtctcttatacacatctgacgctgccgacgaatgtca > SRR3722111.371781/1‑61 (MQ=60)
GGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAAT < SRR3722111.12614/100‑1 (MQ=60)
GTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATT > SRR3722111.150367/1‑100 (MQ=60)
GGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGT > SRR3722111.187160/1‑100 (MQ=60)
cagatgtgtataagagacagGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGG < SRR3722111.317686/80‑1 (MQ=60)
CTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGG > SRR3722111.84296/1‑100 (MQ=60)
TTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > SRR3722111.405298/1‑100 (MQ=60)
TTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCGTC > SRR3722111.281413/1‑100 (MQ=60)
|
GGTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > NZ_CP009273/2536020‑2536203
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
