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 |
2,633,582 |
C→T |
57.2% |
R200R (CGC→CGT) |
livG → |
leucine/isoleucine/valine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,633,582 | 0 | C | T | 57.2%
| 17.6
/ 52.0
| 70 | R200R (CGC→CGT) | livG | leucine/isoleucine/valine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (9/21); new base T (31/9); total (40/30) |
| Fisher's exact test for biased strand distribution p-value = 9.20e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01 |
CGAACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGATATGAAGCTGGTGATGGGAATTT > minE/2633516‑2633643
|
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:981031/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:1975155/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:1991402/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:1837262/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:2641844/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:1350624/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:1171765/69‑1 (MQ=255)
cgaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:236170/69‑1 (MQ=255)
gaACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCaa < 1:2662100/68‑1 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:815791/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:320883/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:688736/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:61147/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:2461650/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:3415576/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:1638010/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:2188357/1‑68 (MQ=255)
gaACCGGCAGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTaac > 1:1921933/1‑68 (MQ=255)
tCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAAcaccac > 1:2710397/1‑69 (MQ=255)
cTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAatca > 1:2462446/1‑56 (MQ=255)
cTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACt > 1:1641603/1‑69 (MQ=255)
cTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACt > 1:1167703/1‑69 (MQ=255)
cccGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATc < 1:3233050/67‑1 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAGCTGCGTAACCATCACAACACCAATATCttgtt > 1:3113578/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACt > 1:2558345/1‑61 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2567161/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2909637/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2580874/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2804912/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2684962/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2822281/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2972294/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2272595/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:3153607/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2188994/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:3231047/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2171162/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:2153632/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:1905807/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:1507594/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:1449848/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:1398398/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:921681/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgtt > 1:1148069/1‑69 (MQ=255)
gAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGTAACCATCACAACACCACTATCttgat > 1:2481566/1‑67 (MQ=255)
aaaGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCttgttg < 1:2321837/69‑1 (MQ=255)
aaaGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCttgttg < 1:37593/69‑1 (MQ=255)
aaaGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCttgttg < 1:1957926/69‑1 (MQ=255)
agagCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa < 1:2996742/69‑1 (MQ=255)
agagCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa < 1:3069994/69‑1 (MQ=255)
agagCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa < 1:792878/69‑1 (MQ=255)
agagCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa < 1:3181177/69‑1 (MQ=255)
gagCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa < 1:226850/68‑1 (MQ=255)
cTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa < 1:1163530/65‑1 (MQ=255)
aGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGa > 1:1498751/1‑58 (MQ=255)
cTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTTATTGAACACGATATGAAGCTGGt < 1:2786019/68‑1 (MQ=255)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:1071323/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:841884/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:1595995/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:3305591/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:3285861/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:2182722/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:313241/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:3025148/40‑1 (MQ=38)
gATTGCCGAACTGCGTAACCATCACAACACCACTATCttg < 1:1034024/40‑1 (MQ=38)
tGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGaa > 1:1199760/1‑46 (MQ=255)
tGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGATATGAAGCTGGTGATggg > 1:449374/1‑69 (MQ=255)
tGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGATATGAAGCTGGTGATggg > 1:2267485/1‑69 (MQ=255)
tGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGATATGAAGCTGGTGATggg > 1:2284006/1‑69 (MQ=255)
aaCTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGATATGAAGCTGGTGATGGGAAttt < 1:1413152/69‑1 (MQ=255)
|
CGAACCTGCGGCAGGTCTTAACCCGAAAGAGACGAAAGAGCTGGATGAGCTGATTGCCGAACTGCGCAATCATCACAACACCACTATCTTGTTGATTGAACACGATATGAAGCTGGTGATGGGAATTT > minE/2633516‑2633643
|
| 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
