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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
716,324 |
C→T |
intergenic (‑46/+188) |
BW25113_RS26090 ← / ← kdpE |
leader peptide SpeFL/two‑component system response regulator KdpE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 716,324 | 0 | C | T | 88.9%
| 103.9
/ 4.2
| 36 | intergenic (‑46/+188) | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
| Reads supporting (aligned to +/- strand): ref base C (1/3); new base T (9/23); total (10/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.70e-01 |
TCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAA > NZ_CP009273/716239‑716407
|
tCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGa > 1:221063/1‑90 (MQ=255)
gCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAAt < 2:438051/90‑1 (MQ=255)
gCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAAt < 1:480302/90‑1 (MQ=255)
cTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATAc < 1:360788/90‑1 (MQ=255)
cTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATAc < 1:374471/90‑1 (MQ=255)
atatGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGt < 1:139019/90‑1 (MQ=255)
atatGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGt < 1:205223/90‑1 (MQ=255)
tGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGa < 2:565994/90‑1 (MQ=255)
tGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGa < 1:406293/90‑1 (MQ=255)
gggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGa < 1:193591/88‑1 (MQ=255)
gggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGa > 2:193591/1‑88 (MQ=255)
gggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAAc > 2:85467/1‑90 (MQ=255)
gggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAAc > 1:267683/1‑90 (MQ=255)
ggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAAt > 2:594939/1‑79 (MQ=255)
ggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAAt < 1:594939/79‑1 (MQ=255)
ggCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACt > 1:548766/1‑90 (MQ=255)
cATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACtgt > 1:48006/1‑90 (MQ=255)
tAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGa < 2:267683/90‑1 (MQ=255)
tAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCCGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGa > 1:7126/1‑90 (MQ=255)
aGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGaa < 2:293068/90‑1 (MQ=255)
gCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGAt < 1:676360/90‑1 (MQ=255)
gCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGAt > 1:137146/1‑90 (MQ=255)
cTGTTATTTTCCATTTAATTTACCTTTCCCGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATc < 2:7126/90‑1 (MQ=255)
gTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCaa > 2:608713/1‑90 (MQ=255)
tttaatttaCCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGAt < 2:702193/90‑1 (MQ=255)
ttaatttaCCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATc < 2:221063/90‑1 (MQ=255)
ttaatttaCCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATc < 2:548766/90‑1 (MQ=255)
tttCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAatt < 1:352670/90‑1 (MQ=255)
tttCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAatt < 2:137146/90‑1 (MQ=255)
tttCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAatt < 1:465335/90‑1 (MQ=255)
tGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAatttattt < 2:48006/90‑1 (MQ=255)
aatgaaGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAatgatg < 1:298827/90‑1 (MQ=255)
aatgaaGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAatgatg < 2:562585/90‑1 (MQ=255)
aatgaaGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAatgatg < 2:590594/90‑1 (MQ=255)
aatgaaGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAatgatg < 2:678489/90‑1 (MQ=255)
gATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTc < 1:383463/90‑1 (MQ=255)
tctatctaGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTaa < 1:608713/90‑1 (MQ=255)
tctatctaGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTaa < 2:731970/90‑1 (MQ=255)
|
TCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAA > NZ_CP009273/716239‑716407
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAATATAAAATATTGAAT > NZ_CP009273/716229‑716422
|
ATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGA > SRR3722073.225641/1‑100 (MQ=60)
acacactgcatatcgtcggcagcgtcagatgtgtataagagacagCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAA < SRR3722073.642176/55‑1 (MQ=60)
GCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAAC > SRR3722073.273340/1‑100 (MQ=60)
GCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAAC < SRR3722073.607344/100‑1 (MQ=60)
GCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAAC < SRR3722073.490516/100‑1 (MQ=60)
CCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACT > SRR3722073.560224/1‑100 (MQ=60)
CTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTG < SRR3722073.368431/100‑1 (MQ=60)
CTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTG < SRR3722073.382422/100‑1 (MQ=60)
TTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGT > SRR3722073.49135/1‑100 (MQ=60)
ATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGA < SRR3722073.141911/100‑1 (MQ=60)
ATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGA < SRR3722073.209400/100‑1 (MQ=60)
ATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCCGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGA > SRR3722073.7308/1‑100 (MQ=60)
TGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGG < SRR3722073.414959/100‑1 (MQ=60)
TGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGG < SRR3722073.197450/100‑1 (MQ=60)
GCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGAT > SRR3722073.139999/1‑100 (MQ=60)
GCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAA < SRR3722073.690192/100‑1 (MQ=60)
TTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGA < SRR3722073.475262/100‑1 (MQ=60)
TTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGA < SRR3722073.360139/100‑1 (MQ=60)
AATGAAGGTGAAGATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTAC < SRR3722073.305146/100‑1 (MQ=60)
GATATTCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAATATAA < SRR3722073.391617/100‑1 (MQ=60)
TCTATCTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAATATAAAATAT < SRR3722073.621398/100‑1 (MQ=60)
CTAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAATATAAAATATTGAAT < SRR3722073.87391/100‑1 (MQ=60)
|
ATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTCCATTTAATTTACCTTTCCTGATGTGAATGAAGGTGAAGATATTCTATCCAGGAAATACGGTTGAACTGTGAAGGTGATCAATAAAAAATGATCAATCTTAATTTATTTAATGATGAGCTTTTTACTCAGTAATATAAAATATTGAAT > NZ_CP009273/716229‑716422
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
