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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
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 | 98.1%
| 165.5
/ ‑6.1
| 52 | D351G (GAC→GGC) | fliK | flagellar hook‑length control protein FliK |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (20/31); total (20/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGA > NZ_CP009273/2012838‑2013001
|
cTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATAc > 1:961545/1‑90 (MQ=255)
cTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATAc < 2:704293/90‑1 (MQ=255)
tCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGt > 1:1059056/1‑90 (MQ=255)
tCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGt > 1:209323/1‑90 (MQ=255)
cagcagcagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCgg < 1:1353643/88‑1 (MQ=255)
cagcagcagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCgg > 2:1353643/1‑88 (MQ=255)
cagcagcagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGtt > 2:162641/1‑90 (MQ=255)
cagcagcagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGtt > 2:411905/1‑90 (MQ=255)
cagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 1:429000/90‑1 (MQ=255)
cagGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 2:1241386/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAACCCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 2:1340089/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 2:1488642/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 2:1399540/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 2:1211725/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 2:386357/90‑1 (MQ=255)
ggCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtctc < 1:387162/90‑1 (MQ=255)
gCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTa > 2:374910/1‑90 (MQ=255)
cccAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAg < 2:767954/90‑1 (MQ=255)
cccAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAg < 2:143701/90‑1 (MQ=255)
ccAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAgg < 1:1520068/90‑1 (MQ=255)
cagcaacagcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAggg < 1:888017/90‑1 (MQ=255)
acagcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCgtgt > 2:1170180/1‑90 (MQ=255)
gcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAAc > 1:990556/1‑90 (MQ=255)
gcaaAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAAc < 2:990556/90‑1 (MQ=255)
cGCACCGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGCTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAgc < 1:1350494/90‑1 (MQ=255)
cGCACAGCAATCCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAgc < 1:1033647/90‑1 (MQ=255)
cGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAgc < 1:297890/90‑1 (MQ=255)
caGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGCGTAACAGGCAACAgcggcg > 2:801223/1‑90 (MQ=255)
aaCCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa > 2:1450343/1‑60 (MQ=255)
aaCCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACaa < 1:1450343/60‑1 (MQ=255)
tGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCg > 2:1489702/1‑60 (MQ=255)
tGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCg < 1:1489702/60‑1 (MQ=255)
tGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATAtttt > 2:442238/1‑90 (MQ=255)
tGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATAtttt > 1:422520/1‑90 (MQ=255)
tGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATAtttt > 1:1242185/1‑90 (MQ=255)
gAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTc < 1:993527/90‑1 (MQ=255)
ctctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCt < 1:1122448/90‑1 (MQ=255)
tctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc > 1:1207621/1‑40 (MQ=255)
tctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGtc < 2:1207621/40‑1 (MQ=38)
tctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTa < 2:248911/90‑1 (MQ=255)
ctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTaa > 1:937875/1‑90 (MQ=255)
ctGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTaa > 2:975522/1‑90 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 2:1392591/90‑1 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 1:162641/90‑1 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 2:231633/90‑1 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 1:411905/90‑1 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 1:1181211/90‑1 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 2:920619/90‑1 (MQ=255)
gggggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 1:1018756/90‑1 (MQ=255)
gggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCaga > 1:470951/1‑90 (MQ=255)
gggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa > 2:1332525/1‑88 (MQ=255)
gggAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCa < 1:1332525/88‑1 (MQ=255)
|
CTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGA > NZ_CP009273/2012838‑2013001
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
|
GTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATAC > SRR3722078.975199/1‑100 (MQ=60)
GCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGT > SRR3722078.1074982/1‑100 (MQ=60)
GCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGT > SRR3722078.211853/1‑100 (MQ=60)
GTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTC < SRR3722078.1375369/100‑1 (MQ=60)
accgagatctacacgaccgccatcgtcggcagcgtcagatgtgtataagagacagGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACA < SRR3722078.1361333/45‑1 (MQ=60)
CAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAG < SRR3722078.434168/100‑1 (MQ=60)
GGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGG < SRR3722078.391877/100‑1 (MQ=60)
cagatgtgtataagagacagACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAA < SRR3722078.1473993/80‑1 (MQ=60)
CCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGGGTAAC > SRR3722078.1004938/1‑100 (MQ=60)
CCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACA < SRR3722078.1544856/100‑1 (MQ=60)
CAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAG < SRR3722078.899955/100‑1 (MQ=60)
cagatgtgtataagagacagCAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGC < SRR3722078.1513991/80‑1 (MQ=60)
CGCACCGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGCTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATA < SRR3722078.1372179/100‑1 (MQ=60)
CGCACAGCAATCCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATA < SRR3722078.1049010/100‑1 (MQ=60)
CGCACAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATA < SRR3722078.301536/100‑1 (MQ=60)
CAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTT > SRR3722078.1261809/1‑100 (MQ=60)
CAGCAAACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTT > SRR3722078.427617/1‑100 (MQ=60)
ACCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGctgtctcttatacacatctgacgctgccgacgatggcggt > SRR3722078.1226590/1‑60 (MQ=60)
CCATGAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAA > SRR3722078.950881/1‑100 (MQ=60)
GAACCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTC < SRR3722078.1007975/100‑1 (MQ=60)
CCTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGA > SRR3722078.476541/1‑100 (MQ=60)
CTCTGGCGGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAG < SRR3722078.1139587/100‑1 (MQ=60)
GGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC < SRR3722078.1353873/100‑1 (MQ=60)
GGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC < SRR3722078.164535/100‑1 (MQ=60)
GGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC < SRR3722078.1199662/100‑1 (MQ=60)
GGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC < SRR3722078.416888/100‑1 (MQ=60)
GGGGGAAGGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCAC < SRR3722078.1033799/100‑1 (MQ=60)
GGCGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATC < SRR3722078.379491/100‑1 (MQ=60)
|
GTGGCGAAAGCTTTAGTGGTCAGCAGCAGGCCGCTTCCCAGCAACAGCAAAGCCAACGCACAGCAAACCATGAACCTCTGGCGGGGGAAGACGACGATACGCTTCCGGTTCCCGTCTCTTTACAAGGGCGTGTAACAGGCAACAGCGGCGTTGATATTTTCGCCTAACGTCAGAGGTAGCACCGTAATC > NZ_CP009273/2012828‑2013016
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
