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 |
1,368,914 |
C→T |
56.5% |
V167V (GTG→GTA) |
dusC ← |
tRNA‑dihydrouridine synthase C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,368,914 | 0 | C | T | 56.5%
| 11.3
/ 45.5
| 61 | V167V (GTG→GTA) | dusC | tRNA‑dihydrouridine synthase C |
| Reads supporting (aligned to +/- strand): ref base C (18/8); new base T (8/26); total (27/34) |
| Fisher's exact test for biased strand distribution p-value = 5.90e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCAAATTTCTTCTCACCGC > minE/1368861‑1368978
|
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:3007885/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:2957926/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:2032384/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:1345688/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:959439/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:932076/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTa > 1:1482968/1‑69 (MQ=255)
gCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGAACCACCAGCTCCGTa > 1:2030884/1‑69 (MQ=255)
ccGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCg < 1:1412516/69‑1 (MQ=255)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:3011844/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:2832758/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:3363670/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:3415749/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:2401277/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:2390484/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:179035/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:1114262/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:1500152/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:1107951/1‑34 (MQ=37)
cgcgGTAACCCTGCTCTTTTGTCCGCCCATGtact > 1:1319290/1‑34 (MQ=37)
gTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:8772/69‑1 (MQ=255)
gTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:1548642/69‑1 (MQ=255)
gTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:1528656/69‑1 (MQ=255)
gTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:1939175/69‑1 (MQ=255)
gTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:3291015/69‑1 (MQ=255)
tAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:2299130/68‑1 (MQ=255)
accccTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTCTTGa > 1:657678/3‑56 (MQ=255)
aaCCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGtt > 1:1072347/1‑54 (MQ=255)
aaCCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGa > 1:1209639/1‑69 (MQ=255)
aaCCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGa > 1:509387/1‑69 (MQ=255)
aaCCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGa > 1:117332/1‑69 (MQ=255)
aaCCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGa > 1:2649399/1‑69 (MQ=255)
aaCCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGa > 1:2567692/1‑69 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTg > 1:3039058/1‑48 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTGTTg > 1:1954068/1‑51 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTGTTg > 1:1048131/1‑51 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTGTTg > 1:487118/1‑51 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTGTTg > 1:2528960/1‑51 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTGTTg > 1:872692/1‑51 (MQ=255)
cTGCTCTTTTGTCCGCCCATGTACTACCAGCTCAGTAGCGCCAGCCTGTTg > 1:1183864/1‑51 (MQ=37)
cTGCTCTTTTGACCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCTGTTg > 1:2304626/1‑51 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:396306/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:3342846/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:622774/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:792338/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:3186300/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:818697/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:831207/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:96520/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2435593/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2900049/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:1542167/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:1691467/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:1996670/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2110566/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2144840/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2182417/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2246715/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:1007077/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2554535/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2735674/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2777512/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2834841/46‑1 (MQ=255)
tGCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:294177/46‑1 (MQ=255)
gCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:2429234/45‑1 (MQ=255)
gCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:3392677/45‑1 (MQ=255)
gCTCTTTTGTCCGCCCATGTACTACCAGCTCCGTAGCGCCAGCCt < 1:1445098/45‑1 (MQ=255)
ctctTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCaaa > 1:774193/1‑69 (MQ=255)
ctctTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCaaa > 1:868111/1‑69 (MQ=255)
ctctTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCaa > 1:1396116/1‑68 (MQ=255)
tctTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGc < 1:620100/59‑1 (MQ=255)
ttCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCAAATttc > 1:1012614/1‑69 (MQ=255)
caccacCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCAAATTTCTTCTCACCGc < 1:1842808/65‑1 (MQ=255)
|
GCCTGCCAGTCAATATGCTCCGCGCGGTAACCCTGCTCTTTCGTCCGCCCATGCACCACCAGCTCCGTAGCGCCAGCCTGTTGAACCGCATCGGCGATTTCAAATTTCTTCTCACCGC > minE/1368861‑1368978
|
| 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
