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 |
|
A2 F1 I1 R1
|
748 |
32.0 |
1685426 |
92.6% |
1560704 |
103.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,474,138 |
(A)6→7 |
coding (15/594 nt) |
bdcR → |
transcriptional repressor for divergent bdcA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,474,132 | 1 | . | A | 97.0%
| 98.1
/ ‑3.2
| 33 | coding (9/594 nt) | bdcR | transcriptional repressor for divergent bdcA |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (15/17); total (16/17) |
| Fisher's exact test for biased strand distribution p-value = 4.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01 |
GCACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑A‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCT > NC_000913/4473995‑4474260
|
gCACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑a > 1:591999/1‑139 (MQ=255)
gACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAAtctc < 2:591999/139‑1 (MQ=255)
aCTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTcg < 2:3705/139‑1 (MQ=255)
cgcCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAgg > 1:507160/1‑139 (MQ=255)
cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAgg < 2:510023/95‑1 (MQ=255)
cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa > 1:586792/1‑139 (MQ=255)
cTTGATTTATTATGCAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑ACAAAAACAATCTCGCGTTCCAgg > 1:510023/1‑95 (MQ=255)
tGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaaaa > 1:66884/1‑139 (MQ=255)
tAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCAc > 2:62083/1‑139 (MQ=255)
cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTcg > 2:79420/1‑69 (MQ=255)
cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTcg < 1:79420/69‑1 (MQ=255)
cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGgt < 1:489310/79‑1 (MQ=255)
cATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGgt > 2:489310/1‑79 (MQ=255)
tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGTTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGgt < 1:834660/77‑1 (MQ=255)
tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATTGTCACTAA‑AAAAACAATCTCGCGTTCCAGgt > 2:834660/1‑77 (MQ=255)
tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa < 2:80345/120‑1 (MQ=255)
tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa > 1:80345/1‑120 (MQ=255)
tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa > 1:222855/1‑139 (MQ=255)
aaaaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGtt < 2:402658/63‑1 (MQ=255)
aaaaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGtt > 1:402658/1‑63 (MQ=255)
aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt < 2:586792/139‑1 (MQ=255)
aGGTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTAc < 2:522999/139‑1 (MQ=255)
ggTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACt < 2:222855/139‑1 (MQ=255)
gTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGc < 1:78017/71‑1 (MQ=255)
gTTTTGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGc > 2:78017/1‑71 (MQ=255)
ttGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt < 2:329494/111‑1 (MQ=255)
ttGTAATGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGAt > 1:329494/1‑111 (MQ=255)
aaTGGTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCt < 2:364102/139‑1 (MQ=255)
ggTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg > 2:20764/1‑56 (MQ=255)
ggTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg < 1:20764/56‑1 (MQ=255)
ggTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCAc < 2:49520/89‑1 (MQ=255)
ggTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCAc > 1:49520/1‑89 (MQ=255)
gTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGa < 2:521199/102‑1 (MQ=255)
gTCACTAA‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGa > 1:521199/1‑102 (MQ=255)
|
GCACCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑A‑AAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCT > NC_000913/4473995‑4474260
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
