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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,230,259 |
C→T |
intergenic (‑86/‑135) |
nhaB ← / → fadR |
Na(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,230,259 | 0 | C | T | 97.4%
| 136.3
/ ‑4.4
| 38 | intergenic (‑86/‑135) | nhaB/fadR | Na(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (19/18); total (19/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.78e-01 |
TTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTC > NZ_CP009273/1230179‑1230345
|
tttCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTc < 2:570524/90‑1 (MQ=255)
ttaccttacAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAgggg > 1:1336140/1‑90 (MQ=255)
tacAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAagag > 1:403855/1‑90 (MQ=255)
acAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAgaga < 2:763479/90‑1 (MQ=255)
taatCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCgg > 1:1228914/1‑90 (MQ=255)
aatCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGa > 1:753312/1‑90 (MQ=255)
aatCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGa < 1:275166/90‑1 (MQ=255)
atCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGaa > 2:961153/1‑90 (MQ=255)
tgatgTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGa < 1:1084007/90‑1 (MQ=255)
atgTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAg < 2:1228914/90‑1 (MQ=255)
ttATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGa < 1:60910/90‑1 (MQ=255)
tGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATcc > 2:937092/1‑90 (MQ=255)
tGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATcc < 2:1532138/90‑1 (MQ=255)
tttAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCt > 2:1098962/1‑90 (MQ=255)
ttAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCtt > 1:612464/1‑90 (MQ=255)
ttAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCtt > 1:1517237/1‑90 (MQ=255)
aaaGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTtcttct > 2:187227/1‑90 (MQ=255)
aaaGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTtcttct > 1:1429063/1‑90 (MQ=255)
aaGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTcttctt > 2:913854/1‑90 (MQ=255)
aGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCttt < 2:1451742/90‑1 (MQ=255)
cGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTg < 2:603050/90‑1 (MQ=255)
taggAGTGAGGCAAGTTTTGATAGTCACGGGGAAAGAGATGCGGAAAATGAAGCCTTGACCCCTTTTTCTTCTTTTTGTCTGCTATCAGc < 1:1117439/89‑1 (MQ=255)
caggAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGc < 1:242212/90‑1 (MQ=255)
caggAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGc < 2:1114071/90‑1 (MQ=255)
caggAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGc < 1:689043/90‑1 (MQ=255)
gAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTa > 1:1126108/1‑90 (MQ=255)
gAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTa > 1:594006/1‑90 (MQ=255)
gAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTa > 2:902828/1‑90 (MQ=255)
gAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTa > 2:436410/1‑90 (MQ=255)
aGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAg > 2:1323605/1‑90 (MQ=255)
aGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAg > 1:285317/1‑90 (MQ=255)
cAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGccc < 1:1460067/90‑1 (MQ=255)
aaGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCct > 2:496992/1‑90 (MQ=255)
aGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTttct < 2:1151108/57‑1 (MQ=255)
aGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCctc < 2:1475774/90‑1 (MQ=255)
aGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCctc < 1:1098962/90‑1 (MQ=255)
aGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCctc < 1:1323605/90‑1 (MQ=255)
aGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCctc < 1:138864/90‑1 (MQ=255)
|
TTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTC > NZ_CP009273/1230179‑1230345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
CAGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATGA > NZ_CP009273/1230160‑1230356
|
CAGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTT > SRR3722078.1093519/1‑100 (MQ=60)
CAGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTC < SRR3722078.47666/100‑1 (MQ=60)
TCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAG < SRR3722078.21541/100‑1 (MQ=60)
ATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGG > SRR3722078.1357558/1‑100 (MQ=60)
TCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAG > SRR3722078.408752/1‑100 (MQ=60)
ACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGG > SRR3722078.1248275/1‑100 (MQ=60)
CCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGA > SRR3722078.762949/1‑100 (MQ=60)
AATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCC < SRR3722078.278520/100‑1 (MQ=60)
TGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATC < SRR3722078.1100412/100‑1 (MQ=60)
GTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTT > SRR3722078.1541981/1‑100 (MQ=60)
GTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTT > SRR3722078.619533/1‑100 (MQ=60)
TTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTC < SRR3722078.61626/100‑1 (MQ=60)
GTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCT > SRR3722078.1452298/1‑100 (MQ=60)
GGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTA > SRR3722078.1143331/1‑100 (MQ=60)
AGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTA > SRR3722078.600900/1‑100 (MQ=60)
GGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAG > SRR3722078.288798/1‑100 (MQ=60)
TAGGAGTGAGGCAAGTTTTGATAGTCACGGGGAAAGAGATGCGGAAAATGAAGCCTTGACCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCC < SRR3722078.1134499/100‑1 (MQ=60)
CAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCC < SRR3722078.245172/100‑1 (MQ=60)
CAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCC < SRR3722078.697188/100‑1 (MQ=60)
GAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCctgtctcttatacacatctgacg > SRR3722078.1168874/1‑77 (MQ=60)
CAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGA < SRR3722078.1483884/100‑1 (MQ=60)
AGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATG < SRR3722078.140477/100‑1 (MQ=60)
AGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATG < SRR3722078.1344763/100‑1 (MQ=60)
AGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATG < SRR3722078.1115690/100‑1 (MQ=60)
GTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATGA > SRR3722078.48225/1‑100 (MQ=60)
|
CAGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGATGA > NZ_CP009273/1230160‑1230356
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
