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 |
1,716,658 |
A→G |
21.8% |
Q370Q (CAA→CAG) |
yphH → |
predicted DNA‑binding transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,716,658 | 0 | A | G | 21.8%
| 52.2
/ 8.8
| 41 | Q370Q (CAA→CAG) | yphH | predicted DNA‑binding transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base A (13/19); new base G (6/3); total (19/22) |
| Fisher's exact test for biased strand distribution p-value = 2.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTATTATTCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGTATG > minE/1716591‑1716716
|
cTATTATTCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCaaa > 1:1005068/1‑69 (MQ=255)
cTATTATTCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCaaa > 1:2305958/1‑69 (MQ=255)
attattCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCAAAtt > 1:742182/1‑69 (MQ=255)
attCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCAAATTGGc > 1:927808/1‑69 (MQ=255)
attCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCAAATTGGc > 1:3028243/1‑69 (MQ=255)
ttAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCAAATTgg > 1:949655/1‑52 (MQ=255)
ttAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGcc < 1:70427/69‑1 (MQ=255)
ttAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGcc < 1:461002/69‑1 (MQ=255)
aCCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGCcgcg > 1:1011330/1‑69 (MQ=255)
aCCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGCcgcg > 1:2860201/1‑69 (MQ=255)
aCCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGCcgcg > 1:2318740/1‑69 (MQ=255)
aCCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGCcgcg > 1:3022366/1‑69 (MQ=255)
aCCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGCcgcg > 1:1968118/1‑69 (MQ=255)
aCCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACACAGATTGGCTTTGGGCAATTAAGCcgcg > 1:3228343/1‑69 (MQ=255)
cgacgaAGGACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCt < 1:557834/69‑1 (MQ=255)
cgacgaAGGACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCt < 1:1024784/69‑1 (MQ=255)
cgacgaAGGACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCt < 1:2759698/69‑1 (MQ=255)
ggACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAAtt > 1:3025459/1‑69 (MQ=255)
ggACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAAtt > 1:1970750/1‑69 (MQ=255)
ggACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAAtt > 1:2872116/1‑69 (MQ=255)
gTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTg < 1:975594/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt > 1:2461080/1‑69 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt > 1:1048635/1‑69 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:1129224/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:1394329/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:152352/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:653537/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:1597186/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:1831808/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:3160293/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt > 1:1831907/1‑69 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt > 1:1872070/1‑69 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:2263308/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:2961396/69‑1 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt > 1:2423284/1‑69 (MQ=255)
tGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt > 1:2495168/1‑69 (MQ=255)
tGAAAGCGACACAGATTGGCTTTGGGCAATTAAGcc < 1:2409667/36‑1 (MQ=37)
gAAAGCGACGCAAATTGGGTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:1570509/68‑1 (MQ=255)
gAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:1698604/68‑1 (MQ=255)
gAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:521420/68‑1 (MQ=255)
gAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGt < 1:847202/68‑1 (MQ=255)
aGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGTATg < 1:696449/68‑1 (MQ=255)
aGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGTATg < 1:951730/68‑1 (MQ=255)
|
CTATTATTCGCCAGACAGGATTTAACCCGTTCGACCGCGACGAAGGACCGAGCGTGAAAGCGACGCAAATTGGCTTTGGGCAATTAAGCCGCGCACAACAGGTGCTGGGAATTGGCTATTTGTATG > minE/1716591‑1716716
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
