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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 91.3%
| 61.4
/ ‑0.8
| 23 | S315S (TCA→TCC) | xylH | xylose ABC transporter permease XylH |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (9/12); total (10/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.55e-01 |
CACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGC > NZ_CP009273/3727940‑3728108
|
cACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTc > 2:316186/1‑90 (MQ=255)
gCCGGGTTCGCGAGTAACGGATTAATGGTCGCCATCGCCGTTTTAATCCTTAGTTGTCGCCGTGGCGCTGGGTCCCCTTCTGCGGGAAat > 2:761992/1‑90 (MQ=255)
gtTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGc > 1:726574/1‑90 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 1:38091/90‑1 (MQ=255)
aaCGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGAc < 1:680726/90‑1 (MQ=255)
aGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATg < 1:784404/90‑1 (MQ=255)
gCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTAGACGCAATTGCAGCATGc < 1:232691/90‑1 (MQ=255)
cGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGAt < 1:624732/90‑1 (MQ=255)
cGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGAt < 2:355770/90‑1 (MQ=255)
aaTCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCAc < 1:653273/90‑1 (MQ=255)
aaTCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCAc > 2:576255/1‑90 (MQ=255)
aTCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCAcc < 1:451057/90‑1 (MQ=255)
ttAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGcc < 2:149070/90‑1 (MQ=255)
tAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCATCAGCct > 2:485053/1‑90 (MQ=255)
tAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCct > 1:708398/1‑90 (MQ=255)
tctcGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGAc < 2:199500/51‑1 (MQ=255)
tctcGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGAc > 1:199500/1‑51 (MQ=255)
cGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCtggctggc > 2:334364/1‑90 (MQ=255)
cGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCtggctggc > 2:428531/1‑90 (MQ=255)
cGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCtggctggc > 1:791233/1‑90 (MQ=255)
gACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCg < 2:255158/90‑1 (MQ=255)
aCTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCgg < 2:791233/90‑1 (MQ=255)
ggTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGc < 2:236406/90‑1 (MQ=255)
|
CACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGC > NZ_CP009273/3727940‑3728108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCAGTA > NZ_CP009273/3727928‑3728123
|
atgtgtataagagacagAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCT < SRR3722079.109785/83‑1 (MQ=60)
TAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCT < SRR3722079.566603/100‑1 (MQ=60)
TTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGC < SRR3722079.810232/100‑1 (MQ=60)
AACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGC > SRR3722079.734348/1‑100 (MQ=60)
AACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAG < SRR3722079.38372/100‑1 (MQ=60)
AACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAG < SRR3722079.687877/100‑1 (MQ=60)
AGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGC < SRR3722079.792813/100‑1 (MQ=60)
GCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTAGACGCAATTGCAGCATGCGTGATTGGCG < SRR3722079.234661/100‑1 (MQ=60)
CGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACC < SRR3722079.631102/100‑1 (MQ=60)
GATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCT > SRR3722079.715920/1‑100 (MQ=60)
AATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCT < SRR3722079.660037/100‑1 (MQ=60)
AATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCtgtctcttatacacatctccgagcccac > SRR3722079.201224/1‑72 (MQ=60)
ATCCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTG < SRR3722079.455004/100‑1 (MQ=60)
CCTTAGTTCTCGACTTGGCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGG > SRR3722079.799711/1‑100 (MQ=60)
GCGCTGGTTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGC > SRR3722079.647326/1‑100 (MQ=60)
TTCCCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCA > SRR3722079.114968/1‑100 (MQ=60)
CCCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCAGTA > SRR3722079.825040/1‑100 (MQ=60)
|
TAACGTTGAACGCACCAAACTTGCCGTGTTCGCGATTAACGGATTAATGGTAGCCATCGCCGGATTAATCCTTAGTTCTCGACTTGGCGCTGGTTCACCTTCTGCGGGAAATATCGCCGAACTGGACGCAATTGCAGCATGCGTGATTGGCGGCACCAGCCTGGCTGGCGGTGTGGGAAGCGTTGCCGGAGCAGTA > NZ_CP009273/3727928‑3728123
|
| 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: ‑ |
