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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,328,974 |
G→C |
P384A (CCA→GCA) |
yfaA ← |
DUF2138 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,328,974 | 0 | G | C | 90.5%
| 61.3
/ 0.4
| 21 | P384A (CCA→GCA) | yfaA | DUF2138 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (2/0); new base C (12/7); total (14/7) |
| Fisher's exact test for biased strand distribution p-value = 5.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.55e-01 |
GAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTC > NZ_CP009273/2328896‑2329043
|
gAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCt > 2:840727/1‑90 (MQ=255)
gAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCt > 2:751619/1‑90 (MQ=255)
gCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGc > 1:34786/1‑90 (MQ=255)
ccGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGc > 2:101727/1‑90 (MQ=255)
acCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTg < 1:632787/90‑1 (MQ=255)
ccTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGa > 2:637698/1‑90 (MQ=255)
cTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGAc > 1:301434/1‑90 (MQ=255)
cTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGAc > 2:309961/1‑90 (MQ=255)
ttCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGAcc > 1:533226/1‑90 (MQ=255)
gctttCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCgg < 1:639813/90‑1 (MQ=255)
aaTATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGa > 1:519942/1‑90 (MQ=255)
atatTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAg < 1:210291/90‑1 (MQ=255)
atatTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAg < 2:34786/90‑1 (MQ=255)
ttGCGTAAACCGTTTCCCTGCCAACTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTc < 2:573535/90‑1 (MQ=255)
ttGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTc > 1:733010/1‑90 (MQ=255)
ttGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGAcc > 2:11535/1‑57 (MQ=255)
ttGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGAcc < 1:11535/57‑1 (MQ=255)
ttGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTc < 1:98565/90‑1 (MQ=255)
ttGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTc > 1:557725/1‑90 (MQ=255)
ttGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTc > 2:826206/1‑90 (MQ=255)
ttGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGGGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGGCTTc > 1:338185/1‑90 (MQ=255)
|
GAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTC > NZ_CP009273/2328896‑2329043
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTCGCCCTGCTGAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTCATACCAGCACAGCCCCGCG > NZ_CP009273/2328885‑2329062
|
TTCGCCCTGCTGAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCC < SRR3722072.612255/100‑1 (MQ=60)
GCTGAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGC > SRR3722072.35409/1‑100 (MQ=60)
GGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGAC > SRR3722072.306660/1‑100 (MQ=60)
GCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACC > SRR3722072.542833/1‑100 (MQ=60)
ACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAAC < SRR3722072.644087/100‑1 (MQ=60)
tcggagatgtgtataagagacaGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGC < SRR3722072.11751/78‑1 (MQ=60)
GCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAAT < SRR3722072.651229/100‑1 (MQ=60)
CGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGA > SRR3722072.529296/1‑100 (MQ=60)
CACCAATATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTC > SRR3722072.746009/1‑100 (MQ=60)
CACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTC > SRR3722072.567748/1‑100 (MQ=60)
CACCAATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGGGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGGCTTC > SRR3722072.344129/1‑100 (MQ=60)
ATATTTTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTCATACC < SRR3722072.213873/100‑1 (MQ=60)
TTGCGTAAACAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTCATACCAGCAC < SRR3722072.100388/100‑1 (MQ=60)
CAGTTTCCCTGCCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTCATACCctgtctcttataca > SRR3722072.392142/1‑86 (MQ=60)
|
TTCGCCCTGCTGAGTCTGGCTTACCGGCAAAACACCTTCTGGCGCTTTGCTTTCGTGCGCACCAATATTTTGCGTAAACAGTTTCCCTGGCAATTGCGCCTGTTCGGCAGTGCCATCAAACTGACCGACAAACAGCGGGGTTTGCAATTTTGAGTCTTCATACCAGCACAGCCCCGCG > NZ_CP009273/2328885‑2329062
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
