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 |
1,312,382 |
T→C |
46.6% |
R336R (CGT→CGC) |
hisD → |
bifunctional histidinal dehydrogenase and histidinol dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,312,382 | 0 | T | C | 46.6%
| 4.7
/ 61.6
| 73 | R336R (CGT→CGC) | hisD | bifunctional histidinal dehydrogenase and histidinol dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (25/14); new base C (11/23); total (36/37) |
| Fisher's exact test for biased strand distribution p-value = 9.80e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
TGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGACTGGTCACCGGAAT > minE/1312320‑1312443
|
tGCGTGGATATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:2139071/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:572413/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:2217879/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:2149720/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:923571/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:2577119/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:1839544/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:1507161/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:433166/69‑1 (MQ=255)
tGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:3396548/69‑1 (MQ=255)
ttgagaTCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCTTGAACTGTTc < 1:732953/66‑1 (MQ=255)
tGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTc < 1:1401733/68‑1 (MQ=255)
tGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTc < 1:3119987/68‑1 (MQ=255)
tGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTc < 1:1749919/68‑1 (MQ=255)
tGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTc < 1:781036/68‑1 (MQ=255)
ggAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTc < 1:1553831/67‑1 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:720693/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:2485731/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:530505/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:385561/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:373672/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:2765312/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:2786834/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:2831902/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:2917882/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:77656/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:3172455/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:1303589/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:1310129/1‑59 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCAt > 1:311046/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAAc > 1:2470381/1‑56 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:1383171/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:3094935/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:3004423/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:1588603/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:1711087/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:3159761/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:1424219/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:261642/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:2500662/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCAt > 1:1219115/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCAGTGAACTGGTCGATAGCAt > 1:1701413/1‑69 (MQ=255)
ctcCAACCAGTACGGCCCGGAGCACCTAATCATTCAGACCCGCAACGCCCGTGAACTgg > 1:2242784/1‑59 (MQ=255)
aCCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATc < 1:465296/65‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:3085517/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:3253324/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:474404/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:1522628/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:109831/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:2474099/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:1921264/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:2129595/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:2621967/59‑1 (MQ=255)
gTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:2099685/59‑1 (MQ=255)
aCGGCCCGGAGGACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:818062/57‑1 (MQ=255)
ggCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTg < 1:2794614/45‑1 (MQ=255)
gCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGCGAACTGGTCGATGGCa < 1:3259077/54‑1 (MQ=39)
cGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCgg < 1:2191234/69‑1 (MQ=255)
gCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGt < 1:711575/66‑1 (MQ=255)
gCACCTGATCATTCAGACCCGCAACGCCCGTAAACTGGTCGATAGCATCACCAGCGCCGGTTCGGt < 1:706480/66‑1 (MQ=255)
cACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGt < 1:2707932/65‑1 (MQ=255)
gATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCgg < 1:1922651/59‑1 (MQ=255)
aTCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGt > 1:944814/1‑69 (MQ=255)
aTCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGt > 1:1235110/1‑69 (MQ=255)
aTCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGt > 1:823329/1‑69 (MQ=255)
aTTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGAc > 1:1187069/1‑69 (MQ=255)
aTTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGAc > 1:3349730/1‑69 (MQ=255)
aTTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGAc > 1:2954298/1‑69 (MQ=255)
aTTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGAc > 1:2179190/1‑69 (MQ=255)
aTTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGAc > 1:1366784/1‑69 (MQ=255)
cAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGACTGGTCACCGGa < 1:2692190/69‑1 (MQ=255)
cAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGACTGGTCACCGGa < 1:2138563/69‑1 (MQ=255)
aCGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGACTGGTCACCGGAAt > 1:2777495/1‑69 (MQ=255)
|
TGCGTGGAGATCTCCAACCAGTACGGCCCGGAGCACCTGATCATTCAGACCCGCAACGCCCGTGAACTGGTCGATAGCATCACCAGCGCCGGTTCGGTATTTCTTGGTGACTGGTCACCGGAAT > minE/1312320‑1312443
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
