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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
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%
| 36.3
/ NA
| 12 | F232S (TTC→TCC) | yqeI | transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (4/8); total (4/8) |
GTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACC > NZ_CP009273/2982478‑2982640
|
gTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCaaa > 1:247933/1‑90 (MQ=255)
gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc > 1:339770/1‑90 (MQ=255)
aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg < 2:188248/90‑1 (MQ=255)
atatAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatgat < 2:185253/90‑1 (MQ=255)
cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa > 1:187885/1‑90 (MQ=255)
tAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGa < 1:439602/90‑1 (MQ=255)
tAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGa < 2:339770/90‑1 (MQ=255)
aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa < 2:322027/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGGAGTGGCAAAc < 1:265449/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 1:391469/90‑1 (MQ=255)
ataCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAc < 2:270863/90‑1 (MQ=255)
taCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAcc > 1:208698/1‑90 (MQ=255)
|
GTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACC > NZ_CP009273/2982478‑2982640
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCT > NZ_CP009273/2982456‑2982646
|
TAACAGAAGATACAATTGATGAGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTC < SRR3722087.186426/100‑1 (MQ=60)
CAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAA > SRR3722087.250322/1‑100 (MQ=60)
GGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACC > SRR3722087.343561/1‑100 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA > SRR3722087.189542/1‑100 (MQ=60)
TAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAC < SRR3722087.444748/100‑1 (MQ=60)
TCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACC > SRR3722087.210522/1‑100 (MQ=60)
CCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGGAGTGGCAAACTGTTTAACCC < SRR3722087.268056/100‑1 (MQ=60)
CCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC < SRR3722087.395997/100‑1 (MQ=60)
TGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGT > SRR3722087.54597/1‑100 (MQ=60)
GTTATACTCCCCTCTTGCAAAATCCTCACCCGGGATGATTGTTATGGCATGCAATAGAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCT > SRR3722087.49440/1‑100 (MQ=60)
|
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCT > NZ_CP009273/2982456‑2982646
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
