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 |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,692,839 |
G→A |
77.4% |
G425D (GGT→GAT) |
ydgA → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,692,839 | 0 | G | A | 77.4%
| 120.1
/ 35.0
| 62 | G425D (GGT→GAT) | ydgA | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (5/9); new base A (34/14); total (39/23) |
| Fisher's exact test for biased strand distribution p-value = 2.68e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCA > W3110S.gb/1692783‑1692897
|
gACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAg < 1:2753230/68‑1 (MQ=255)
gACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAg < 1:3332067/68‑1 (MQ=255)
gACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGa < 1:1013584/69‑1 (MQ=255)
gACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGa < 1:1770270/69‑1 (MQ=255)
cATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCa > 1:3087498/1‑69 (MQ=255)
ccGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGc > 1:3172482/1‑68 (MQ=255)
ccGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGc > 1:3386472/1‑68 (MQ=255)
ccGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGc > 1:2960866/1‑68 (MQ=255)
ccGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGc > 1:1512940/1‑68 (MQ=255)
ccGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGc > 1:2276045/1‑68 (MQ=255)
gATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGaaaaaa > 1:2344041/1‑69 (MQ=255)
gATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGaaaaaa > 1:2513844/1‑69 (MQ=255)
gCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGc > 1:156983/1‑68 (MQ=255)
gCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGc > 1:1361830/1‑68 (MQ=255)
aaCTGAGTTTATGACTCATGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa < 1:2363401/68‑1 (MQ=255)
aCTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGaaa < 1:2094778/69‑1 (MQ=255)
tGAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa > 1:806222/1‑65 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa > 1:765194/1‑64 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa < 1:3553997/64‑1 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa < 1:2904068/64‑1 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGa > 1:1396573/1‑64 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:3597379/1‑68 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:342129/1‑68 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:1070045/1‑68 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:3612266/1‑68 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:3719894/1‑68 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:458913/1‑68 (MQ=255)
gAGTTTATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACa > 1:698035/1‑68 (MQ=255)
tttATGACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCa < 1:3428304/68‑1 (MQ=255)
gACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTg < 1:2364011/68‑1 (MQ=255)
gACTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTg < 1:142905/68‑1 (MQ=255)
aCTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa < 1:2026599/68‑1 (MQ=255)
aCTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa < 1:2022433/68‑1 (MQ=255)
cTCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa < 1:2168847/67‑1 (MQ=255)
tCAGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAgg < 1:2342535/69‑1 (MQ=255)
aGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGaa < 1:376137/40‑1 (MQ=255)
aGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg > 1:1890226/1‑69 (MQ=255)
aGGTAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTg > 1:1433996/1‑69 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:933790/1‑61 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:1316904/1‑61 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:1836623/1‑61 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:2947822/1‑61 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:2007498/1‑61 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:2622066/1‑61 (MQ=255)
tAGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACCGGCGAAACAGCAAGTTGa > 1:1950117/1‑61 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCa < 1:2695431/54‑1 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCa < 1:2387921/54‑1 (MQ=255)
aGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATc > 1:3197029/1‑69 (MQ=255)
aGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATc > 1:2996733/1‑69 (MQ=255)
aGCGAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATc > 1:3545780/1‑69 (MQ=255)
gCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCa < 1:3073988/53‑1 (MQ=255)
gCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATc > 1:2566342/1‑68 (MQ=255)
gAAGCTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGc < 1:2780618/69‑1 (MQ=255)
aaGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCa < 1:2420387/69‑1 (MQ=255)
aaGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCa < 1:2676766/69‑1 (MQ=255)
aaGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCa < 1:899352/69‑1 (MQ=255)
cTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:2078183/1‑35 (MQ=255)
cTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:2073953/1‑35 (MQ=255)
cTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:620243/1‑35 (MQ=255)
cTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:2968662/1‑35 (MQ=255)
cTGGAAGATTATCAGGAAGATCAAGCGAAAAAACt > 1:807180/1‑35 (MQ=255)
cTGGAAGATTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGa > 1:3679850/1‑53 (MQ=255)
|
GACCATTCCGGTGGATATGGCAACTGAGTTTATGACTCAGGTAGCGAAGCTGGAAGGTTATCAGGAAGATCAAGCGAAAAAACTGGCGAAACAGCAAGTTGAAGGTGCATCAGCA > W3110S.gb/1692783‑1692897
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
