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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
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%
| 84.8
/ NA
| 26 | S315S (TCA→TCC) | xylH | xylose ABC transporter permease XylH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (15/11); total (15/11) |
ACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCG > NZ_CP009273/3727937‑3728109
|
aCGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTcccc < 1:289523/90‑1 (MQ=255)
cACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTc > 1:389732/1‑90 (MQ=255)
cACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTc > 2:171119/1‑90 (MQ=255)
ccAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTg < 2:251207/90‑1 (MQ=255)
tGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGaaa > 1:75437/1‑90 (MQ=255)
gCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAat > 1:119165/1‑90 (MQ=255)
gtTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGc < 2:54740/90‑1 (MQ=255)
gtTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGc > 1:54740/1‑90 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 2:465545/90‑1 (MQ=255)
cGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGc < 1:399841/90‑1 (MQ=255)
aTTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAAt > 2:361841/1‑90 (MQ=255)
ggTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcagc < 2:125505/90‑1 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg > 2:449628/1‑90 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg > 2:295693/1‑90 (MQ=255)
aTCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTg > 1:237235/1‑90 (MQ=255)
tCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGa > 2:97704/1‑90 (MQ=255)
ggATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTggc < 2:71566/90‑1 (MQ=255)
gATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTggcg > 2:444451/1‑90 (MQ=255)
aaTCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCAc < 1:449628/90‑1 (MQ=255)
ttAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGcc < 1:302099/90‑1 (MQ=255)
tctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag > 1:57916/1‑61 (MQ=255)
tctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag < 2:57916/61‑1 (MQ=255)
tcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGTCGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggctgg < 2:265483/90‑1 (MQ=255)
tcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggctgg > 1:514476/1‑90 (MQ=255)
ggTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGc > 2:14937/1‑90 (MQ=255)
ggTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGc > 2:507669/1‑90 (MQ=255)
gTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCg < 2:119165/90‑1 (MQ=255)
|
ACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCG > NZ_CP009273/3727937‑3728109
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
ATTAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGG > NZ_CP009273/3727926‑3728098
|
ATTAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCC > SRR3722114.357250/1‑100 (MQ=60)
ACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTC < SRR3722114.271313/100‑1 (MQ=60)
ACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTC > SRR3722114.394457/1‑100 (MQ=60)
ACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGA < SRR3722114.292590/100‑1 (MQ=60)
GCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAA > SRR3722114.76224/1‑100 (MQ=60)
CACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAAT > SRR3722114.120429/1‑100 (MQ=60)
AACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGC > SRR3722114.55283/1‑100 (MQ=60)
CGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCA < SRR3722114.404696/100‑1 (MQ=60)
GATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTG > SRR3722114.239484/1‑100 (MQ=60)
AATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATctgtctcttatacacatct > SRR3722114.58485/1‑81 (MQ=60)
AATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCT < SRR3722114.455218/100‑1 (MQ=60)
TCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGG > SRR3722114.520926/1‑100 (MQ=60)
TTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGG < SRR3722114.305326/100‑1 (MQ=60)
|
ATTAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGG > NZ_CP009273/3727926‑3728098
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
