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 |
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%
| 38.7
/ NA
| 13 | E121G (GAA→GGA) | BW25113_RS09050 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/2); total (11/2) |
TGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806944‑1807108
|
tGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTggg > 2:154873/1‑90 (MQ=255)
aaTTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATa > 2:33290/1‑90 (MQ=255)
gTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAg > 2:419976/1‑90 (MQ=255)
tCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTg < 1:210504/90‑1 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCa > 1:298162/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:581010/1‑90 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATaaa > 1:117588/1‑90 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATaaa > 1:323838/1‑90 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACct > 2:52886/1‑90 (MQ=255)
aaTTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCAt > 1:494219/1‑90 (MQ=255)
ttagTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATaa < 1:496638/87‑1 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGa > 1:361654/1‑90 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGa > 2:421656/1‑90 (MQ=255)
|
TGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806944‑1807108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAA > NZ_CP009273/1806959‑1807115
|
TCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTC < SRR3722111.213081/100‑1 (MQ=60)
ATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCA > SRR3722111.302006/1‑100 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722111.590121/1‑100 (MQ=60)
ATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAA > SRR3722111.119067/1‑100 (MQ=60)
ATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAA > SRR3722111.328152/1‑100 (MQ=60)
ATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCAT > SRR3722111.501819/1‑100 (MQ=60)
GATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > SRR3722111.366693/1‑100 (MQ=60)
TTAGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAA < SRR3722111.504281/100‑1 (MQ=60)
|
TCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAA > NZ_CP009273/1806959‑1807115
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
