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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 85.2%
| 57.5
/ 4.0
| 27 | F232S (TTC→TCC) | yqeI | transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base T (0/4); new base C (6/17); total (6/21) |
| Fisher's exact test for biased strand distribution p-value = 5.45e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
TGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGT > NZ_CP009273/2982475‑2982644
|
tGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGc > 2:307589/1‑90 (MQ=255)
gTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCaaa > 2:660076/1‑90 (MQ=255)
aaaGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATcc < 1:725694/90‑1 (MQ=255)
aaaGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATcc < 1:53559/90‑1 (MQ=255)
agTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAc < 1:672710/90‑1 (MQ=255)
gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc > 1:396574/1‑90 (MQ=255)
ttCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCg < 2:806905/90‑1 (MQ=255)
ttCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCg < 1:641720/90‑1 (MQ=255)
gATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCgggg > 2:816660/1‑90 (MQ=255)
aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGgatg < 2:390417/90‑1 (MQ=255)
aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg < 2:557065/90‑1 (MQ=255)
atatAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGgatgat < 1:398905/90‑1 (MQ=255)
atatAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGgatgat < 1:644285/90‑1 (MQ=255)
atatAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatgat < 1:660076/90‑1 (MQ=255)
atatAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatgat < 2:433472/90‑1 (MQ=255)
cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa > 1:496358/1‑90 (MQ=255)
ggATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCAt < 2:496358/90‑1 (MQ=255)
gATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATg < 2:203555/90‑1 (MQ=255)
aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa < 1:690372/90‑1 (MQ=255)
tCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaaa < 2:475020/90‑1 (MQ=255)
ccGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 1:515814/90‑1 (MQ=255)
ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc < 2:504067/90‑1 (MQ=255)
ggTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGtt > 1:414129/1‑90 (MQ=255)
aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 2:273102/90‑1 (MQ=255)
aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 2:396574/90‑1 (MQ=255)
aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 1:539070/90‑1 (MQ=255)
aCTCCCCTCCTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc < 1:153542/90‑1 (MQ=255)
tCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGt > 1:537759/1‑90 (MQ=255)
|
TGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGT > NZ_CP009273/2982475‑2982644
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGTCTTACCG > NZ_CP009273/2982456‑2982651
|
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTC < SRR3722079.721844/100‑1 (MQ=60)
ACAG‑AGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCC < SRR3722079.601659/100‑1 (MQ=60)
GGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACC > SRR3722079.399894/1‑100 (MQ=60)
AAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGA < SRR3722079.733458/100‑1 (MQ=60)
AAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGA < SRR3722079.53981/100‑1 (MQ=60)
AGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGAT < SRR3722079.679754/100‑1 (MQ=60)
TTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTG < SRR3722079.648340/100‑1 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA < SRR3722079.402257/100‑1 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA < SRR3722079.650941/100‑1 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA < SRR3722079.666931/100‑1 (MQ=60)
ATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCA > SRR3722079.500772/1‑100 (MQ=60)
ggagatgtgtataagagacaGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAG < SRR3722079.843170/80‑1 (MQ=60)
AAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTT > SRR3722079.417687/1‑100 (MQ=60)
ATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑C < SRR3722079.697628/100‑1 (MQ=60)
CCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCC < SRR3722079.520544/100‑1 (MQ=60)
TGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGT > SRR3722079.542817/1‑100 (MQ=60)
TGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCctg > SRR3722079.691256/1‑97 (MQ=60)
GTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCCTGTC > SRR3722079.497652/1‑100 (MQ=60)
GTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGTCT > SRR3722079.36903/1‑100 (MQ=60)
GTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGTCT > SRR3722079.429396/1‑100 (MQ=60)
ACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGTCTTACCG < SRR3722079.544156/100‑1 (MQ=60)
ACTCCCCTCCTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGTCTTACCG < SRR3722079.154873/100‑1 (MQ=60)
|
TAACAGAAGATACAATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAA‑CCCTGTCTTACCG > NZ_CP009273/2982456‑2982651
|
| 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: ‑ |
