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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 55.4
/ NA
| 18 | S315S (TCA→TCC) | xylH | xylose ABC transporter permease XylH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (9/9); total (9/9) |
CGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGC > NZ_CP009273/3727938‑3728108
|
cGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCt < 2:88530/90‑1 (MQ=255)
cGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCt < 2:143748/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 2:276237/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc > 1:76701/1‑90 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc > 1:27721/1‑90 (MQ=255)
tAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTgg > 1:49893/1‑75 (MQ=255)
tAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTgg < 2:49893/75‑1 (MQ=255)
ggATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTggc < 2:38487/90‑1 (MQ=255)
ttAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcagca > 1:371741/1‑68 (MQ=255)
ttAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcagca < 2:371741/68‑1 (MQ=255)
tAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCct > 2:18208/1‑90 (MQ=255)
tAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCct > 2:395996/1‑90 (MQ=255)
ctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag > 1:306439/1‑60 (MQ=255)
ctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTgcag < 2:306439/60‑1 (MQ=255)
ctcGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCctggctg > 1:46055/1‑90 (MQ=255)
gACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCg < 1:214618/90‑1 (MQ=255)
gACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCg < 2:311191/90‑1 (MQ=255)
ggTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGc > 2:310680/1‑90 (MQ=255)
|
CGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGC > NZ_CP009273/3727938‑3728108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
TAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCAGT > NZ_CP009273/3727928‑3728122
|
acagGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCT < SRR3722092.269195/96‑1 (MQ=60)
TAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCT < SRR3722092.425326/100‑1 (MQ=60)
GTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAC > SRR3722092.28204/1‑100 (MQ=60)
GTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAC > SRR3722092.78017/1‑100 (MQ=60)
GGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCctgtc > SRR3722092.50737/1‑95 (MQ=60)
GGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGctgtctcttata > SRR3722092.378749/1‑88 (MQ=60)
ATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATctgtctcttatacacatctg > SRR3722092.311838/1‑80 (MQ=60)
ATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTG > SRR3722092.46843/1‑100 (MQ=60)
GACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAG < SRR3722092.218153/100‑1 (MQ=60)
CCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCAGG > SRR3722092.433100/1‑100 (MQ=60)
|
TAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCAGT > NZ_CP009273/3727928‑3728122
|
| 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: ‑ |
