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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
587,468 |
A→C |
D389E (GAT→GAG) |
nrfB ← |
cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 587,468 | 0 | A | C | 93.1%
| 91.8
/ ‑0.7
| 29 | D389E (GAT→GAG) | nrfB | cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (12/15); total (13/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.28e-01 |
ATGCGGTTAACCATCAAACCAAAGTTTAGCCACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGC > NZ_CP009273/587382‑587554
|
aTGCGGTTAACCATCAAACCAAAGTTTAGCCACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCg > 2:851309/1‑90 (MQ=255)
acaGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCcagcaacagca < 2:410637/90‑1 (MQ=255)
acaGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCcagcaacagca < 1:616605/90‑1 (MQ=255)
cagcagGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCcagcaacagcaa > 2:498507/1‑90 (MQ=255)
cagcagGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCcagcaacagcaa > 1:574891/1‑90 (MQ=255)
aTTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGatc > 1:191623/1‑90 (MQ=255)
ttAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGatca < 1:667871/90‑1 (MQ=255)
tAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGatcat > 2:332016/1‑90 (MQ=255)
aTGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGat > 2:335658/1‑82 (MQ=255)
aTGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGat < 1:335658/82‑1 (MQ=255)
aTGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCa > 2:711143/1‑90 (MQ=255)
aTGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCAAGCAACAGCAAAAGCTGGATCATCACCa > 2:67076/1‑90 (MQ=255)
aTGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCcagcaa > 2:288249/1‑67 (MQ=255)
aTGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCcagcaa < 1:288249/67‑1 (MQ=255)
gcgcTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGc > 2:69562/1‑90 (MQ=255)
cGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGa < 2:540299/90‑1 (MQ=255)
aaaTAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGc < 1:140777/90‑1 (MQ=255)
aGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGAc < 1:173094/90‑1 (MQ=255)
aGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGAc < 2:280653/90‑1 (MQ=255)
aaaGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACaa < 1:674573/90‑1 (MQ=255)
aaaGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACaa < 1:332016/90‑1 (MQ=255)
aaaTGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTa < 1:92750/90‑1 (MQ=255)
aaTGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTAc < 1:117282/90‑1 (MQ=255)
aaTGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTAc > 1:315707/1‑90 (MQ=255)
aaTGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTAc < 1:116095/90‑1 (MQ=255)
cAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGAtt > 2:40445/1‑90 (MQ=255)
ggCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTg > 2:396769/1‑45 (MQ=255)
ggCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTg < 1:396769/45‑1 (MQ=255)
ggCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGc < 1:851309/90‑1 (MQ=255)
|
ATGCGGTTAACCATCAAACCAAAGTTTAGCCACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGC > NZ_CP009273/587382‑587554
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ 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
AGTTTAGCCACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGG > NZ_CP009273/587404‑587564
|
AGTTTAGCCACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAA > SRR3722072.585166/1‑100 (MQ=60)
tgttaagagacaggcCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGC < SRR3722072.293228/85‑1 (MQ=60)
ACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGAT < SRR3722072.627597/100‑1 (MQ=60)
CAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATC > SRR3722072.194946/1‑100 (MQ=60)
cgtctcgtgggctcggaaatgtgtaaaagagacagGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACC < SRR3722072.403928/65‑1 (MQ=60)
CATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGC < SRR3722072.341565/100‑1 (MQ=60)
TTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCAT < SRR3722072.679814/100‑1 (MQ=60)
AAATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTT < SRR3722072.143297/100‑1 (MQ=60)
ATAGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTAC > SRR3722072.321227/1‑100 (MQ=60)
AGAAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTG < SRR3722072.176091/100‑1 (MQ=60)
AAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGAT < SRR3722072.686651/100‑1 (MQ=60)
AAAGGAAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGAT < SRR3722072.337845/100‑1 (MQ=60)
AAATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCC < SRR3722072.94459/100‑1 (MQ=60)
AATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCC < SRR3722072.119441/100‑1 (MQ=60)
AATGCCAGGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCC < SRR3722072.118228/100‑1 (MQ=60)
CACGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGC < SRR3722072.818393/100‑1 (MQ=60)
GGCCTCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGG < SRR3722072.866023/100‑1 (MQ=60)
|
AGTTTAGCCACAGCAGGGTCATTAACCATGCGCTGCCGCTGAAAATAGAAAGGAAATGCCAGGCATCGGGCCACAAACTTTCATACGCCAGCAACAGCAAAAGCTGGATCATCACCAGCATCGCGAGGAAGCTGACAAAGTTACTGATTGCCCCTTTGCGG > NZ_CP009273/587404‑587564
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
