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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
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 | 97.6%
| 139.8
/ ‑2.9
| 42 | 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 (18/23); total (19/23) |
| Fisher's exact test for biased strand distribution p-value = 4.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > NZ_CP009273/3934909‑3935075
|
gTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑cccccgc < 2:532203/90‑4 (MQ=18)
ccTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGaaaaa > 2:957058/1‑90 (MQ=255)
ccTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAaaag > 2:535898/1‑90 (MQ=33)
gagaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagca > 2:748409/1‑90 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa > 2:968924/1‑90 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa > 2:940202/1‑90 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa > 2:207606/1‑90 (MQ=255)
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaagc < 2:552209/90‑1 (MQ=255)
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaagc < 1:174421/90‑1 (MQ=255)
aCTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaagc < 1:511101/90‑1 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCg > 1:1041163/1‑90 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCg > 1:361579/1‑90 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑cccccgc > 1:606091/1‑65 (MQ=25)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑cccccgc < 2:606091/68‑4 (MQ=25)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 1:1002833/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 2:925974/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 2:544190/1‑90 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:1026277/90‑1 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 1:1209614/90‑1 (MQ=255)
cAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAc < 1:637943/90‑1 (MQ=255)
gCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGa < 2:1012560/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 1:789475/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 2:141198/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 2:753318/90‑1 (MQ=255)
gACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAAt < 1:1090441/90‑1 (MQ=255)
aCTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATc < 2:901329/90‑1 (MQ=255)
aCTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATc < 1:764795/90‑1 (MQ=255)
ctctGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCt < 2:847084/90‑1 (MQ=255)
gTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgtgt > 2:717406/1‑90 (MQ=255)
cGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGc < 1:1114497/90‑1 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 1:85139/76‑1 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc > 2:85139/1‑76 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 2:735197/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:781988/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 2:1090754/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:860336/1‑90 (MQ=255)
ggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCAc < 2:831100/90‑1 (MQ=255)
aGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGa > 1:260771/1‑90 (MQ=255)
aGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGa < 2:882513/90‑1 (MQ=255)
ttatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATAc < 1:484449/90‑1 (MQ=255)
tatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACg < 2:577447/90‑1 (MQ=255)
tatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACg < 1:150423/90‑1 (MQ=255)
tatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACg < 1:171634/90‑1 (MQ=255)
tGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGa < 2:1026504/90‑1 (MQ=255)
gCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAt > 1:771940/1‑90 (MQ=255)
|
GTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > NZ_CP009273/3934909‑3935075
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGAC > NZ_CP009273/3934896‑3935092
|
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCC < SRR3722089.400258/100‑1 (MQ=8)
GCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGC < SRR3722089.1002133/100‑1 (MQ=7)
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGActgtctcttata > SRR3722089.613601/1‑88 (MQ=8)
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCG > SRR3722089.1056752/1‑100 (MQ=24)
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCG > SRR3722089.366036/1‑100 (MQ=24)
CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC > SRR3722089.1017746/1‑100 (MQ=24)
ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTC < SRR3722089.517118/100‑1 (MQ=24)
ACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTC < SRR3722089.176602/100‑1 (MQ=24)
GCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAAC < SRR3722089.1228001/100‑1 (MQ=24)
CAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAG < SRR3722089.646079/100‑1 (MQ=24)
acaGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTG < SRR3722089.86184/97‑1 (MQ=24)
CTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTG < SRR3722089.800308/100‑1 (MQ=24)
GACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGC < SRR3722089.1106893/100‑1 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722089.872634/1‑100 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722089.792654/1‑100 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA < SRR3722089.775067/100‑1 (MQ=24)
GTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGA > SRR3722089.264114/1‑100 (MQ=24)
CGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAT < SRR3722089.1131372/100‑1 (MQ=24)
AGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > SRR3722089.782385/1‑100 (MQ=8)
GCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATT > SRR3722089.1140204/1‑100 (MQ=6)
GCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATGTTTCAGACAATCTGTGTGGGCACTCGAAGGTACTGATT > SRR3722089.1232752/1‑100 (MQ=4)
GTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCT > SRR3722089.644807/1‑100 (MQ=6)
GTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCT > SRR3722089.389348/1‑100 (MQ=6)
GTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCT > SRR3722089.796255/1‑100 (MQ=6)
TATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTT > SRR3722089.50536/1‑100 (MQ=6)
TTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAA < SRR3722089.490201/100‑1 (MQ=6)
TATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAAC < SRR3722089.152291/100‑1 (MQ=6)
TATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAAC < SRR3722089.173784/100‑1 (MQ=6)
ATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG > SRR3722089.1075451/1‑100 (MQ=6)
C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > SRR3722089.183129/1‑100 (MQ=7)
C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > SRR3722089.877825/1‑100 (MQ=7)
CCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGAC > SRR3722089.90379/1‑100 (MQ=7)
|
AACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAGAC > NZ_CP009273/3934896‑3935092
|
| 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: ‑ |
