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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,012,918 |
A→G |
D351G (GAC→GGC) |
fliK → |
flagellar hook‑length control protein FliK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,012,918 | 0 | A | G | 100.0%
| 93.3
/ NA
| 28 | D351G (GAC→GGC) | fliK | flagellar hook‑length control protein FliK |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/16); total (12/16) |
GAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGT > NZ_CP009273/2012833‑2013004
|
gAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAggcgac > 2:665422/1‑90 (MQ=255)
cTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATAc < 2:1111425/90‑1 (MQ=255)
cTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATAc < 1:677330/90‑1 (MQ=255)
ttAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGc < 2:581953/90‑1 (MQ=255)
ttAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGc > 2:264744/1‑90 (MQ=255)
gTCAGCAGCAGGCCGCTTCCCAGCAACAGCGAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCgg > 1:803973/1‑90 (MQ=255)
cagcagcagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGtt > 1:634934/1‑90 (MQ=255)
gcagcagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTcc < 1:842994/90‑1 (MQ=255)
cagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 2:935678/90‑1 (MQ=255)
cagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 2:199806/90‑1 (MQ=255)
cagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 2:1049923/90‑1 (MQ=255)
cagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 1:238113/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 1:1020931/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc > 1:135010/1‑90 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 1:196669/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 1:415859/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 2:377860/90‑1 (MQ=255)
tCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa < 1:709933/90‑1 (MQ=255)
acagcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCgtgt < 1:218574/90‑1 (MQ=255)
acagcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTCACAAGGGCgtgt > 2:916672/1‑90 (MQ=255)
gcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAAc > 1:498043/1‑90 (MQ=255)
gcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAAc < 2:822648/90‑1 (MQ=255)
caGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAgcggcg > 1:760193/1‑90 (MQ=255)
ctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTaa > 2:284307/1‑90 (MQ=255)
ctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTaa > 1:395229/1‑90 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 2:728543/90‑1 (MQ=255)
gggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCaga > 2:139849/1‑90 (MQ=255)
gggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCaga > 1:489300/1‑90 (MQ=255)
aaGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGt > 2:170440/1‑90 (MQ=255)
|
GAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGT > NZ_CP009273/2012833‑2013004
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
GTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATC > NZ_CP009273/2012828‑2013016
|
agGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATAC < SRR3722089.1169887/98‑1 (MQ=60)
GGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCGAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGG > SRR3722089.815136/1‑100 (MQ=60)
CTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTT < SRR3722089.686118/100‑1 (MQ=60)
CTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTT > SRR3722089.643018/1‑100 (MQ=60)
GTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTC > SRR3722089.136651/1‑100 (MQ=60)
GCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTA < SRR3722089.854957/100‑1 (MQ=60)
CAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAG < SRR3722089.241139/100‑1 (MQ=60)
GGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGG < SRR3722089.420891/100‑1 (MQ=60)
GGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGG < SRR3722089.199152/100‑1 (MQ=60)
GGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGG < SRR3722089.1036146/100‑1 (MQ=60)
TCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAA < SRR3722089.719178/100‑1 (MQ=60)
CCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAAC > SRR3722089.503943/1‑100 (MQ=60)
ACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAAC < SRR3722089.221346/100‑1 (MQ=60)
AGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCG > SRR3722089.770343/1‑100 (MQ=60)
CCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAA > SRR3722089.400041/1‑100 (MQ=60)
CCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGA > SRR3722089.495102/1‑100 (MQ=60)
GGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAG > SRR3722089.360275/1‑100 (MQ=60)
GGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATC < SRR3722089.287947/100‑1 (MQ=60)
|
GTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATC > NZ_CP009273/2012828‑2013016
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
