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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
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 | 100.0%
| 85.7
/ NA
| 29 | intergenic (‑304/‑177) | yieP/BW25113_RS19520 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (13/16); total (13/16) |
GTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAT > NZ_CP009273/3934918‑3935069
|
gTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTgag > 1:220103/1‑90 (MQ=255)
ccTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTACGCACACCCCCGCGCCGCTGAGaaaaa > 1:366683/1‑90 (MQ=11)
tGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagc < 1:250486/90‑1 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa < 2:98326/90‑1 (MQ=255)
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAaaagcaaa > 1:171160/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 2:131203/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 1:248371/1‑90 (MQ=255)
ccGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGc > 1:292991/1‑90 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:232313/90‑1 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc > 2:374934/1‑90 (MQ=255)
agagAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGc < 2:309047/90‑1 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACaa < 1:469506/90‑1 (MQ=255)
aaataaatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAAt > 2:63090/1‑90 (MQ=255)
taaatGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTa < 1:374934/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 2:366683/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 2:295124/90‑1 (MQ=255)
ttGACTCTGTAGCGGGAAAGCGTATTATGCCCACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACa < 2:223626/90‑1 (MQ=11)
tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa < 2:240751/90‑1 (MQ=255)
tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa < 1:63090/90‑1 (MQ=255)
tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa > 2:215914/1‑90 (MQ=255)
tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa < 1:424383/90‑1 (MQ=255)
tGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACaa < 1:19372/90‑1 (MQ=255)
gACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAAt < 2:363417/90‑1 (MQ=255)
ctGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt > 1:445064/1‑61 (MQ=255)
ctGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACt < 2:445064/61‑1 (MQ=255)
cGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGc < 2:410541/90‑1 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:242374/1‑90 (MQ=255)
aGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGa > 1:49766/1‑90 (MQ=255)
tattatGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAt > 1:456154/1‑90 (MQ=255)
|
GTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAT > NZ_CP009273/3934918‑3935069
|
| 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
GGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > NZ_CP009273/3934908‑3935090
|
GGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG > SRR3722113.221876/1‑100 (MQ=7)
GCGGGGGTTTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTACGCACACCCCCGCGGCGCTGAGAAAAA > SRR3722113.370470/1‑100 (MQ=5)
GTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAA > SRR3722113.172536/1‑100 (MQ=19)
CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC > SRR3722113.250519/1‑100 (MQ=24)
CCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGC > SRR3722113.295723/1‑100 (MQ=24)
TGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCAC < SRR3722113.252663/100‑1 (MQ=24)
AAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAC < SRR3722113.474484/100‑1 (MQ=24)
TAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATC < SRR3722113.378823/100‑1 (MQ=24)
ggctcggagatgtgtataagagacagGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTG < SRR3722113.113195/74‑1 (MQ=7)
ATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACctgtctcttatacacatct > SRR3722113.449777/1‑81 (MQ=26)
TGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGG < SRR3722113.63650/100‑1 (MQ=24)
TGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGG < SRR3722113.428864/100‑1 (MQ=24)
TGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGG < SRR3722113.19551/100‑1 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722113.244461/1‑100 (MQ=24)
GTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGA > SRR3722113.50181/1‑100 (MQ=24)
CGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAT > SRR3722113.460977/1‑100 (MQ=24)
CGTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTC > SRR3722113.300747/1‑100 (MQ=6)
GTATTATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCT > SRR3722113.398615/1‑100 (MQ=6)
ATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG > SRR3722113.357998/1‑100 (MQ=6)
ATGCACACCCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACG > SRR3722113.220728/1‑100 (MQ=6)
C‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > SRR3722113.419709/1‑100 (MQ=7)
|
GGTCAGCGGGGTTCTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAGAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAACGTCGCAAG > NZ_CP009273/3934908‑3935090
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
