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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,807,028 |
T→C |
E121G (GAA→GGA) |
BW25113_RS09050 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,807,028 | 0 | T | C | 100.0%
| 39.3
/ NA
| 13 | E121G (GAA→GGA) | BW25113_RS09050 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/4); total (9/4) |
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806947‑1807108
|
atataATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa < 1:59186/90‑1 (MQ=255)
aTTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATAc < 1:121902/90‑1 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa > 1:335251/1‑90 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa > 1:598018/1‑90 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa > 2:404334/1‑90 (MQ=255)
atataGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCa > 1:241628/1‑90 (MQ=255)
taGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTc < 1:404334/90‑1 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 2:262957/1‑90 (MQ=255)
gAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCtttat > 1:266219/1‑90 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACct > 1:358633/1‑90 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACct > 2:510489/1‑90 (MQ=255)
aaaTTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCa < 2:429986/90‑1 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGa > 1:371385/1‑90 (MQ=255)
|
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806947‑1807108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806945‑1807108
|
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGA > SRR3722088.338745/1‑100 (MQ=60)
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGA > SRR3722088.605376/1‑100 (MQ=60)
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAG < SRR3722088.59815/100‑1 (MQ=60)
ATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACA < SRR3722088.123165/100‑1 (MQ=60)
TGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCA > SRR3722088.244003/1‑100 (MQ=60)
TAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATC < SRR3722088.408760/100‑1 (MQ=60)
CTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTAT > SRR3722088.268796/1‑100 (MQ=60)
GTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCT > SRR3722088.362433/1‑100 (MQ=60)
GATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > SRR3722088.375324/1‑100 (MQ=60)
|
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806945‑1807108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
