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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,934,995 |
+C |
intergenic (‑308/‑173) |
yieP ← / → BW25113_RS19520 |
FadR/GntR family transcriptional regulator/16S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,934,991 | 1 | . | C | 96.0%
| 75.6
/ ‑4.3
| 25 | intergenic (‑304/‑177) | yieP/BW25113_RS19520 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (13/11); total (14/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑A‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAG > NZ_CP009273/3934918‑3935067
|
gTTCTCCTGAGAACTCCGGCAGAGAAAGTAACAATAAATGCGTGACTCTGTAGAGGGAGATCGTATTATGCACAA‑CCCCGCGCCGCTgag > 2:565601/1‑90 (MQ=11)
gTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTgag > 2:550778/1‑90 (MQ=255)
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAaaagcaaagc < 1:145084/90‑1 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCg > 2:162641/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 1:99213/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 2:298261/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 2:266435/1‑90 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 1:421857/90‑1 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 1:117981/90‑1 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc > 2:575483/1‑90 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc < 1:275285/90‑1 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc < 2:530944/90‑1 (MQ=255)
aatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATc < 2:66139/90‑1 (MQ=255)
tGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAg < 1:378730/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 2:87010/90‑1 (MQ=255)
aCTCTGTAGCGGGAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATc < 2:621152/90‑1 (MQ=255)
gggAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 2:203783/1‑90 (MQ=255)
gggAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 2:237255/1‑90 (MQ=255)
gggAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:304386/1‑90 (MQ=255)
gggAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 2:121006/1‑90 (MQ=255)
gggAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:94985/1‑90 (MQ=255)
gggAAAGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:320891/1‑90 (MQ=255)
aGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa > 2:175453/1‑73 (MQ=255)
aGCGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa < 1:175453/73‑1 (MQ=255)
cGTATTATGCAC‑ACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAg < 1:522934/90‑1 (MQ=255)
|
GTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCAC‑A‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAG > NZ_CP009273/3934918‑3935067
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ 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
GCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > NZ_CP009273/3934901‑3935090
|
GCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGC < SRR3722088.216916/100‑1 (MQ=7)
GCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGC < SRR3722088.657427/100‑1 (MQ=7)
GCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGC < SRR3722088.476191/100‑1 (MQ=7)
CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC > SRR3722088.100234/1‑100 (MQ=24)
catacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTC < SRR3722088.324143/48‑1 (MQ=20)
ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTC < SRR3722088.146564/100‑1 (MQ=24)
GCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAC < SRR3722088.119194/100‑1 (MQ=24)
GCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAC < SRR3722088.426566/100‑1 (MQ=24)
AGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAA < SRR3722088.277941/100‑1 (MQ=24)
TGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTG < SRR3722088.382754/100‑1 (MQ=24)
gagacagGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGG < SRR3722088.177211/93‑1 (MQ=25)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722088.95943/1‑100 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722088.324163/1‑100 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722088.307399/1‑100 (MQ=24)
CGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTC < SRR3722088.529256/100‑1 (MQ=6)
GTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCT > SRR3722088.392593/1‑100 (MQ=6)
GTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCT > SRR3722088.58407/1‑100 (MQ=6)
C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > SRR3722088.143282/1‑100 (MQ=7)
|
GCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > NZ_CP009273/3934901‑3935090
|
| 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: ‑ |
