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 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,657,292 |
G→A |
45.9% |
E521E (GAG→GAA) |
ppk → |
polyphosphate kinase, component of RNA degradosome |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,657,292 | 0 | G | A | 45.9%
| 5.8
/ 38.5
| 50 | E521E (GAG→GAA) | ppk | polyphosphate kinase, component of RNA degradosome |
| Reads supporting (aligned to +/- strand): ref base G (11/16); new base A (9/14); total (20/30) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
ACATTTGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAA > minE/1657224‑1657357
|
aCATTTGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCgag < 1:3421427/69‑1 (MQ=255)
aCATTTGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCgag < 1:458031/69‑1 (MQ=255)
tGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCg > 1:1129629/1‑68 (MQ=255)
tGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCg > 1:586280/1‑68 (MQ=255)
tGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCg > 1:709756/1‑68 (MQ=255)
attattTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGcc < 1:602663/68‑1 (MQ=255)
aTCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAg < 1:3333505/68‑1 (MQ=255)
aTCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAg < 1:3237913/68‑1 (MQ=255)
aTCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAg < 1:1929005/68‑1 (MQ=255)
aTCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAg < 1:1786376/68‑1 (MQ=255)
gcAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGcc < 1:1597698/69‑1 (MQ=255)
gcAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGcc < 1:2083062/69‑1 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:3209531/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:785441/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg < 1:713941/69‑1 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:1572911/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:1410758/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:2299615/1‑69 (MQ=255)
cTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTgg > 1:3039124/1‑69 (MQ=255)
tCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGt < 1:1402753/69‑1 (MQ=255)
gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa < 1:825714/69‑1 (MQ=255)
gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa < 1:1664296/69‑1 (MQ=255)
gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa < 1:1026363/69‑1 (MQ=255)
gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa < 1:2577504/69‑1 (MQ=255)
gccgccTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCa < 1:2621787/69‑1 (MQ=255)
gTATGAAATGGTGGACCGCGAGATCGCCAACGCgcagc < 1:3114814/38‑1 (MQ=255)
gTATGAAATGGTGGACCGCGAGATAGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGc > 1:2675420/1‑68 (MQ=255)
gTATGAAATGGTGGAC‑‑CGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTa > 1:1619275/1‑68 (MQ=255)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCTGTATCACCCTGAAGCTAAAt < 1:1297991/59‑1 (MQ=38)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCTGTATCACCCTGAAGCTAAAt < 1:1938562/59‑1 (MQ=38)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:844739/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:3394529/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:516596/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:647412/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:3085999/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:1130276/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:199335/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:2112694/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:2220352/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:2293788/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:2453252/59‑1 (MQ=39)
aCCGCGAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAAt < 1:3091592/59‑1 (MQ=39)
ccGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGa < 1:1982773/69‑1 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:464025/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:300742/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:593911/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:40419/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:624458/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:367593/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:3430817/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:1799385/1‑69 (MQ=255)
cgAAATCGCCAACGCGCAGCAAGGGCTGCCCAGCGGTATCACCCTGAAGCTAAATAACCTTGTCGATaa > 1:1288114/1‑69 (MQ=255)
|
ACATTTGATTATTTAATGGTATCGCCGCAAAACTCCCGCCGCCTATTGTATGAAATGGTGGACCGCGAGATCGCCAACGCGCAGCAAGGGCTGCCCAGTGGTATCACCCTGAAGCTAAATAACCTTGTCGATAA > minE/1657224‑1657357
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
