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 |
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 | 96.4%
| 82.5
/ ‑3.5
| 28 | F232S (TTC→TCC) | yqeI | transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (11/16); total (11/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
AATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC > NZ_CP009273/2982469‑2982641
|
aaTTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTcccc > 1:372714/1‑90 (MQ=255)
tGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCctct < 1:41532/90‑1 (MQ=255)
gATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCtt > 2:419767/1‑90 (MQ=255)
gATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCtt > 2:376804/1‑90 (MQ=255)
tGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAAt > 1:94041/1‑90 (MQ=255)
aaaGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATcc < 2:559716/90‑1 (MQ=255)
gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc > 2:214607/1‑90 (MQ=255)
gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc > 2:49937/1‑90 (MQ=255)
ttCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCg > 1:366306/1‑90 (MQ=255)
cGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCggg < 1:411178/90‑1 (MQ=255)
aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg < 1:214607/90‑1 (MQ=255)
aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg < 2:354532/90‑1 (MQ=255)
aaaaCACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATc < 1:441951/71‑1 (MQ=255)
aaaaCACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATc > 2:441951/1‑71 (MQ=255)
cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa > 1:633402/1‑90 (MQ=255)
cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa > 2:451473/1‑90 (MQ=255)
ggATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaa < 1:484529/90‑1 (MQ=255)
tCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAAc > 1:125388/1‑90 (MQ=255)
aaaaaCATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAg < 2:402488/90‑1 (MQ=255)
aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa < 2:118889/90‑1 (MQ=255)
tCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaaa > 1:32544/1‑90 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:636646/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:571241/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:372714/90‑1 (MQ=255)
ccGTGATTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 1:611105/90‑1 (MQ=255)
gTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGttt < 1:550518/90‑1 (MQ=255)
aCTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 1:385558/90‑1 (MQ=255)
aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 2:233378/90‑1 (MQ=255)
aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 2:105116/90‑1 (MQ=255)
|
AATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC > NZ_CP009273/2982469‑2982641
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTG > NZ_CP009273/2982456‑2982653
|
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTC < SRR3722088.325175/100‑1 (MQ=60)
CAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCC > SRR3722088.376674/1‑100 (MQ=60)
ATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAAT > SRR3722088.94987/1‑100 (MQ=60)
TGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCC < SRR3722088.41959/100‑1 (MQ=60)
GTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCG > SRR3722088.370198/1‑100 (MQ=60)
aagagacagCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGG < SRR3722088.447046/91‑1 (MQ=60)
CGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTT < SRR3722088.415715/100‑1 (MQ=60)
AAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGG < SRR3722088.216763/100‑1 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA > SRR3722088.641235/1‑100 (MQ=60)
GATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAAC > SRR3722088.126689/1‑100 (MQ=60)
GGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAAC < SRR3722088.490295/100‑1 (MQ=60)
GTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAA > SRR3722088.32882/1‑100 (MQ=60)
CCGTGATTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC < SRR3722088.618638/100‑1 (MQ=60)
GTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCT < SRR3722088.557250/100‑1 (MQ=60)
ACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG < SRR3722088.389642/100‑1 (MQ=60)
ACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG < SRR3722088.269035/100‑1 (MQ=60)
ACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCG > SRR3722088.157240/1‑100 (MQ=60)
TCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTG < SRR3722088.42826/100‑1 (MQ=60)
|
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTG > NZ_CP009273/2982456‑2982653
|
| 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: ‑ |
