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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,728,024 |
A→C |
S315S (TCA→TCC) |
xylH → |
xylose ABC transporter permease XylH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,728,024 | 0 | A | C | 100.0%
| 150.5
/ NA
| 44 | S315S (TCA→TCC) | xylH | xylose ABC transporter permease XylH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (21/23); total (21/23) |
GCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGG > NZ_CP009273/3727939‑3728103
|
gCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCtt > 1:646504/1‑90 (MQ=255)
cACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTc > 2:439789/1‑90 (MQ=255)
ccAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTg < 2:542731/90‑1 (MQ=255)
ccAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTg < 2:271645/90‑1 (MQ=255)
gCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAat > 1:250719/1‑90 (MQ=255)
gCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAat > 2:450836/1‑90 (MQ=255)
gCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAat > 1:560732/1‑90 (MQ=255)
gtTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGc < 1:531203/90‑1 (MQ=255)
tAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGa < 1:526150/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 1:195419/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 2:646504/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 2:454450/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 1:679961/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 1:462939/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 1:355172/90‑1 (MQ=255)
aCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGCTCCCCTTCTGCGGGAAATATCGCCGAACTGGACg > 1:656787/1‑90 (MQ=255)
aTTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAAt > 1:597962/1‑90 (MQ=255)
ttAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAAtt < 1:84113/90‑1 (MQ=255)
tGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag < 2:651164/90‑1 (MQ=255)
tAGCCATCGCCGGATTAATCCTTAGTTCTCGTCTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCAt < 2:197738/90‑1 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGc > 2:311785/1‑78 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGc < 1:311785/78‑1 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg > 1:151617/1‑90 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg > 1:223088/1‑90 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg > 2:649112/1‑90 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg > 1:445348/1‑90 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCAAACTGGACGCAATTGCAGCATg > 2:654414/1‑90 (MQ=255)
tCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGa > 2:83133/1‑90 (MQ=255)
gCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGAtt > 2:131813/1‑90 (MQ=255)
aaTCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCAc < 2:148147/90‑1 (MQ=255)
ttAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGcc < 1:444576/90‑1 (MQ=255)
tctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggct < 2:33594/90‑1 (MQ=255)
tctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggct > 1:599413/1‑90 (MQ=255)
cGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCtggctggc > 1:234171/1‑90 (MQ=255)
gACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCg < 2:662608/90‑1 (MQ=255)
cTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGgt < 1:291252/90‑1 (MQ=255)
ttGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGgtg < 1:472451/90‑1 (MQ=255)
ttGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGgtg < 1:72340/90‑1 (MQ=255)
tGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc > 1:78132/1‑43 (MQ=255)
tGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 2:78132/43‑1 (MQ=255)
tGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGgtgt > 1:43396/1‑90 (MQ=255)
tGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGgtgt > 2:93927/1‑90 (MQ=255)
tGGCGCTGGCTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGgtgt > 1:405759/1‑90 (MQ=255)
gcgcTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTgg < 1:28392/90‑1 (MQ=255)
|
GCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGG > NZ_CP009273/3727939‑3728103
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGC > NZ_CP009273/3727929‑3728113
|
AACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTT > SRR3722112.656575/1‑100 (MQ=60)
CACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAAT > SRR3722112.253681/1‑100 (MQ=60)
CACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAAT > SRR3722112.569232/1‑100 (MQ=60)
GTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAC < SRR3722112.539079/100‑1 (MQ=60)
TTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGCTCCCCTTCTGCGGGAAATATCGCCGAACTGGACG > SRR3722112.667035/1‑100 (MQ=60)
CGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAAT > SRR3722112.607117/1‑100 (MQ=60)
TAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGC‑ATTGCAG < SRR3722112.533917/100‑1 (MQ=60)
AACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAG < SRR3722112.197806/100‑1 (MQ=60)
AACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAG < SRR3722112.690594/100‑1 (MQ=60)
AACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAG < SRR3722112.469501/100‑1 (MQ=60)
AACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAG < SRR3722112.359685/100‑1 (MQ=60)
AGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCA < SRR3722112.315355/100‑1 (MQ=60)
GATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATG > SRR3722112.451532/1‑100 (MQ=60)
GATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATG > SRR3722112.225772/1‑100 (MQ=60)
GATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATG > SRR3722112.153488/1‑100 (MQ=60)
TTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCG < SRR3722112.85153/100‑1 (MQ=60)
AATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCT > SRR3722112.608590/1‑100 (MQ=60)
CCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGC > SRR3722112.236977/1‑100 (MQ=60)
TTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGG < SRR3722112.450741/100‑1 (MQ=60)
GTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCtgtctcttatacacatctgacgctgccgacgaatgt > SRR3722112.79081/1‑64 (MQ=60)
GTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGT > SRR3722112.43920/1‑100 (MQ=60)
GTTCTCGACTTGGCGCTGGCTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGT > SRR3722112.411118/1‑100 (MQ=60)
CTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCG < SRR3722112.294625/100‑1 (MQ=60)
TTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGT < SRR3722112.479190/100‑1 (MQ=60)
TTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGT < SRR3722112.73220/100‑1 (MQ=60)
GCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGC < SRR3722112.28750/100‑1 (MQ=60)
|
AACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGC > NZ_CP009273/3727929‑3728113
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
