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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,982,555 |
T→C |
F232S (TTC→TCC) |
yqeI → |
transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,982,555 | 0 | T | C | 100.0%
| 128.1
/ NA
| 36 | F232S (TTC→TCC) | yqeI | transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/24); total (12/24) |
TGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC > NZ_CP009273/2982472‑2982641
|
tGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCctct < 2:641595/90‑1 (MQ=255)
agTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAc < 2:27874/90‑1 (MQ=255)
gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc > 2:464789/1‑90 (MQ=255)
gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc > 2:711570/1‑90 (MQ=255)
ttCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCg > 2:339317/1‑90 (MQ=255)
aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg < 2:567648/90‑1 (MQ=255)
aaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatga < 1:287590/90‑1 (MQ=255)
aaaaCACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGtt > 1:173916/1‑90 (MQ=255)
aaaaCACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGtt > 2:59062/1‑90 (MQ=255)
cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa > 1:654421/1‑90 (MQ=255)
ggATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCAt > 1:653090/1‑90 (MQ=255)
ggATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCAt < 2:75742/90‑1 (MQ=255)
gATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATg > 2:184932/1‑90 (MQ=255)
gATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATg < 1:231566/90‑1 (MQ=255)
tACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCa < 2:714217/90‑1 (MQ=255)
tGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATa < 2:476324/90‑1 (MQ=255)
ggATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg > 1:333135/1‑70 (MQ=255)
ggATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg < 2:333135/70‑1 (MQ=255)
ggATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaa > 2:652717/1‑90 (MQ=255)
gATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaaa < 1:339317/90‑1 (MQ=255)
gATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaaa < 2:296897/90‑1 (MQ=255)
ggggATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACta < 1:184932/90‑1 (MQ=255)
aTTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAAc > 2:599254/1‑90 (MQ=255)
tAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGa < 1:714944/90‑1 (MQ=255)
tAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGa < 1:599254/90‑1 (MQ=255)
aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa < 1:738105/90‑1 (MQ=255)
aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa < 1:734335/90‑1 (MQ=255)
aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa < 2:741578/90‑1 (MQ=255)
tCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaaa > 1:697466/1‑90 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:15776/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:653090/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:95344/90‑1 (MQ=255)
ggTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGtt < 2:445074/90‑1 (MQ=255)
ttATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTa < 2:85471/90‑1 (MQ=255)
ataCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAc < 2:199889/90‑1 (MQ=255)
aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 2:696123/90‑1 (MQ=255)
|
TGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC > NZ_CP009273/2982472‑2982641
|
| 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
CAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG > NZ_CP009273/2982459‑2982651
|
CAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCC < SRR3722073.563464/100‑1 (MQ=60)
AAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCT < SRR3722073.767264/100‑1 (MQ=60)
GATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTG < SRR3722073.584190/100‑1 (MQ=60)
CGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTT > SRR3722073.177312/1‑100 (MQ=60)
AATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGC < SRR3722073.293678/100‑1 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA > SRR3722073.667852/1‑100 (MQ=60)
TATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCAT > SRR3722073.666506/1‑100 (MQ=60)
CACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCtgtctctta > SRR3722073.340210/1‑91 (MQ=60)
GATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAAC < SRR3722073.236403/100‑1 (MQ=60)
GATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACC < SRR3722073.346520/100‑1 (MQ=60)
GGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACAT < SRR3722073.188538/100‑1 (MQ=60)
GTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAA > SRR3722073.711624/1‑100 (MQ=60)
TAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAC < SRR3722073.611745/100‑1 (MQ=60)
TAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAC < SRR3722073.729390/100‑1 (MQ=60)
ATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAC < SRR3722073.749196/100‑1 (MQ=60)
ATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAC < SRR3722073.753040/100‑1 (MQ=60)
TGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGT > SRR3722073.160252/1‑100 (MQ=60)
ACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG < SRR3722073.203778/100‑1 (MQ=60)
|
CAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG > NZ_CP009273/2982459‑2982651
|
| 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: ‑ |
