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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,223,232 |
(A)8→7 |
coding (63/294 nt) |
BW25113_RS06140 → |
YcgL domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,223,225 | 0 | A | . | 89.3%
| 82.8
/ 9.9
| 28 | coding (56/294 nt) | BW25113_RS06140 | YcgL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (2/1); new base . (16/9); total (18/10) |
| 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 |
TATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGG > NZ_CP009273/1223136‑1223312
|
tATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGa > 2:1404599/1‑90 (MQ=255)
aTGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaa > 2:156288/1‑90 (MQ=255)
tGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaaa > 1:700737/1‑90 (MQ=255)
tGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaaaaa > 2:938252/1‑82 (MQ=255)
tGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaaaaa < 1:938252/82‑1 (MQ=255)
cTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTcg > 2:311330/1‑90 (MQ=255)
aaaGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 2:700737/90‑1 (MQ=255)
aaaGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 2:432411/90‑1 (MQ=255)
gTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTcc > 2:567389/1‑90 (MQ=255)
aTGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc > 2:78863/1‑90 (MQ=255)
aTGTCTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc > 2:1294428/1‑90 (MQ=255)
gTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGa > 2:691835/1‑86 (MQ=255)
gTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGa < 1:691835/86‑1 (MQ=255)
gTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACtg > 2:1038501/1‑90 (MQ=255)
ttGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACtgatg > 1:1014231/1‑90 (MQ=255)
ttGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACtgatg > 1:133522/1‑90 (MQ=255)
gtgtgATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGaa > 1:295801/1‑90 (MQ=255)
ttATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGtt > 2:1039210/1‑66 (MQ=255)
ttATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGtt < 1:1039210/66‑1 (MQ=255)
aTCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTgg < 1:567389/90‑1 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 1:80997/90‑1 (MQ=255)
cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc < 1:787370/90‑1 (MQ=255)
gACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCga > 2:1459562/1‑90 (MQ=255)
aCCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTc > 2:65516/1‑90 (MQ=255)
tATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt > 2:1132160/1‑35 (MQ=38)
tATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt < 1:1132160/35‑1 (MQ=38)
ttATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGc < 1:1292220/90‑1 (MQ=255)
tatGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGcc < 1:792337/65‑1 (MQ=255)
tatGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGcc > 2:792337/1‑65 (MQ=255)
tatGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTgg > 2:345015/1‑90 (MQ=255)
tatGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCATGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTgg > 1:575708/1‑90 (MQ=255)
tGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGAt > 1:171059/1‑90 (MQ=255)
cGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATgg > 1:503519/1‑90 (MQ=255)
|
TATGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGG > NZ_CP009273/1223136‑1223312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ 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
CCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGGCGGAAGAAACTGGTCA > NZ_CP009273/1223140‑1223329
|
CCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTT < SRR3722078.951266/100‑1 (MQ=60)
ccacgaccgccatcgtcggcagcgtcagatgtgtataagagacaGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGG < SRR3722078.1149497/56‑1 (MQ=60)
tgtataagagacagTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAC < SRR3722078.1054705/86‑1 (MQ=60)
AAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATG > SRR3722078.1029178/1‑100 (MQ=60)
AAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATG > SRR3722078.135064/1‑100 (MQ=60)
AGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAA > SRR3722078.299409/1‑100 (MQ=60)
GTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAA < SRR3722078.700040/100‑1 (MQ=60)
ATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAG < SRR3722078.574037/100‑1 (MQ=60)
CGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTT < SRR3722078.797652/100‑1 (MQ=60)
CGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTT < SRR3722078.81944/100‑1 (MQ=60)
gtgtataagagacggGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCG < SRR3722078.802714/85‑1 (MQ=60)
GACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCATGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGG > SRR3722078.582425/1‑100 (MQ=60)
CCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGAT > SRR3722078.173058/1‑100 (MQ=60)
ATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGG > SRR3722078.509472/1‑100 (MQ=60)
TTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGGCG < SRR3722078.1312790/100‑1 (MQ=60)
AAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGGCGGAAGAAACTGGTCA > SRR3722078.1200564/1‑100 (MQ=60)
|
CCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGGGCGGAAGAAACTGGTCA > NZ_CP009273/1223140‑1223329
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
