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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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%
| 70.4
/ ‑2.6
| 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 = 3.82e-01 |
GAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > NZ_CP009273/3934928‑3935075
|
gaACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAaaagcaaa > 2:346432/1‑90 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTg > 1:414728/1‑75 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTg < 2:414728/75‑1 (MQ=255)
cTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCg > 1:94805/1‑90 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACt < 1:320609/90‑1 (MQ=255)
gCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACt < 2:483625/90‑1 (MQ=255)
gaAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGctct > 2:144907/1‑90 (MQ=255)
gaAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGctcc > 2:448197/1‑89 (MQ=255)
aaaaTAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACaa < 1:138462/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 1:360763/90‑1 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc > 2:586400/1‑90 (MQ=255)
cTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAc < 2:273256/90‑1 (MQ=255)
ctGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCtgt > 2:257777/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:218857/1‑90 (MQ=255)
gggAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCa > 1:62799/1‑90 (MQ=255)
aaaGCGTATTATGCACACCCCCGCGCCGCTGAGAAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACt > 2:408282/1‑90 (MQ=11)
aaaGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTc < 2:122600/90‑1 (MQ=255)
aaaGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTc < 2:109574/90‑1 (MQ=255)
aGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGa > 2:110256/1‑90 (MQ=255)
aGCGTATTATGCACA‑CCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGaa > 2:74553/1‑90 (MQ=35)
cGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGCCACTCGAAg < 1:44809/90‑1 (MQ=11)
gTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGa > 2:248856/1‑90 (MQ=255)
tattatGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGAt < 2:430597/90‑1 (MQ=255)
atGCACACCCCCGCGCCGCTGAGAAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACg < 1:408282/90‑1 (MQ=11)
gCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAt > 2:452106/1‑90 (MQ=255)
|
GAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGAT > NZ_CP009273/3934928‑3935075
|
| 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
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAAC > NZ_CP009273/3934921‑3935082
|
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCActgtc > SRR3722109.420793/1‑95 (MQ=10)
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCG > SRR3722109.95981/1‑100 (MQ=24)
GCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAAC < SRR3722109.324844/100‑1 (MQ=24)
AAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGAC < SRR3722109.140174/100‑1 (MQ=24)
CTTGACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTG < SRR3722109.365748/100‑1 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722109.221482/1‑100 (MQ=24)
ACTCTGTAGCGGGAAAGCGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCA > SRR3722109.63539/1‑100 (MQ=24)
CGTATTATGCACACCCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGCCACTCGAAGATACGGATTC < SRR3722109.45342/100‑1 (MQ=5)
ATGCACACCCCCGCGCCGCTGAGAAAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAAC < SRR3722109.414225/100‑1 (MQ=5)
|
CTCCTGAGAACTCCGGCAGAGAAAGCAAAAATAAATGCTTGACTCTGTAGCGGGAAAGCGTATTATGCACA‑CCCCGCGCCGCTGAG‑AAAAAGCAAAGCGGCACTGCTCTTTAACAATTTATCAGACAATCTGTGTGGGCACTCGAAGATACGGATTCTTAAC > NZ_CP009273/3934921‑3935082
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
