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 I198 R1
|
96 |
36.2 |
2313912 |
84.6% |
1957569 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,782,276 |
T→G |
V192G (GTG→GGG) |
ppsR → |
posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,782,276 | 0 | T | G | 76.9%
| 27.3
/ 3.7
| 13 | V192G (GTG→GGG) | ppsR | posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
| Reads supporting (aligned to +/- strand): ref base T (3/0); new base G (4/6); total (7/6) |
| Fisher's exact test for biased strand distribution p-value = 1.92e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01 |
AAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTC > NZ_CP009273/1782189‑1782365
|
aaaCCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGc < 2:829758/90‑1 (MQ=255)
ccccACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTAcc > 1:452049/1‑90 (MQ=255)
gCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCtt < 2:952731/90‑1 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAg > 2:401011/1‑90 (MQ=255)
gTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATaa > 1:802982/1‑90 (MQ=255)
aTCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTc < 1:98714/90‑1 (MQ=255)
cgcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGc > 2:1152565/1‑90 (MQ=255)
cgcgcgGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGc > 2:104210/1‑90 (MQ=255)
aaCTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATc < 1:25177/90‑1 (MQ=255)
aaCTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATc < 2:349472/90‑1 (MQ=255)
aaTCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 2:381332/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 2:219432/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg < 2:98820/90‑1 (MQ=255)
tGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTc > 2:615135/1‑90 (MQ=255)
|
AAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTC > NZ_CP009273/1782189‑1782365
|
| 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
GTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAACA > NZ_CP009273/1782183‑1782374
|
GTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACC > SRR3722077.460300/1‑100 (MQ=60)
TGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAA > SRR3722077.817749/1‑100 (MQ=60)
ATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTA < SRR3722077.100574/100‑1 (MQ=60)
AACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAAC < SRR3722077.25674/100‑1 (MQ=60)
GGATAATCTGGGGCTGCCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGT > SRR3722077.407362/1‑100 (MQ=60)
ATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGA > SRR3722077.441274/1‑100 (MQ=60)
ATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTAACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGA > SRR3722077.601815/1‑100 (MQ=60)
GTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAACA > SRR3722077.909313/1‑100 (MQ=60)
|
GTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAACA > NZ_CP009273/1782183‑1782374
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
