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 |
1,982,466 |
T→A |
43.9% |
V125V (GTT→GTA) |
yggS → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,982,466 | 0 | T | A | 43.9%
| 8.6
/ 40.2
| 41 | V125V (GTT→GTA) | yggS | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (9/14); new base A (12/6); total (21/20) |
| Fisher's exact test for biased strand distribution p-value = 1.18e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01 |
TTTGCGCATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTGGCTGAACTGG > minE/1982406‑1982527
|
tttGCGCATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCa < 1:990170/69‑1 (MQ=255)
gcATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAAtt < 1:2816730/68‑1 (MQ=255)
gcATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAAtt < 1:569989/68‑1 (MQ=255)
gcATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAAtt < 1:472253/68‑1 (MQ=255)
gcATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAAtt < 1:297049/68‑1 (MQ=255)
gcATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAAtt < 1:1007185/68‑1 (MQ=255)
gcATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAAtt < 1:2032174/68‑1 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:1841518/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:553218/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:2190422/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:505263/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:642291/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:2577272/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:3328236/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:880200/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:3024151/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:916017/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTACTGAt > 1:1214142/1‑59 (MQ=255)
aTCGCTACCCGTCTGAACGACCAGCGCCCGGCAGAACTTACCCCTCTTAACGTACTGAt > 1:2317328/1‑59 (MQ=255)
aTCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTaa < 1:98553/68‑1 (MQ=255)
cAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTaa > 1:760817/1‑68 (MQ=255)
cAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAg > 1:1197833/1‑69 (MQ=255)
cAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAg > 1:552687/1‑69 (MQ=255)
cAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAg > 1:2656453/1‑69 (MQ=255)
cAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAg > 1:2609093/1‑69 (MQ=255)
ggCAGAACTTCCCCCTCTTAACGTACTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGAt < 1:2954797/69‑1 (MQ=255)
ggCAGAACTTCCCCCTCTTAACGTACTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGAt < 1:3205191/69‑1 (MQ=255)
ggCAGAACTTCCCCCTCTTAACGTACTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGAt < 1:2413637/69‑1 (MQ=255)
ggCAGAACTTCCCCCTCTTAACGTACTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGAt < 1:1200975/69‑1 (MQ=255)
ggCAGAACTTCCCCCTCTTAACGTACTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGAt < 1:2263419/69‑1 (MQ=255)
aGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCa < 1:1254445/69‑1 (MQ=255)
aGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCa < 1:2733773/69‑1 (MQ=255)
aGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCa < 1:1364343/69‑1 (MQ=255)
aGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCa < 1:2010797/69‑1 (MQ=255)
aGAACTTCCCCCTCTTAACGTACTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGAt < 1:199504/66‑1 (MQ=255)
cTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTg > 1:2104245/1‑69 (MQ=255)
cccTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGGTTCAACTGGCTg < 1:1167597/68‑1 (MQ=255)
cccTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTGGCTg < 1:3351637/68‑1 (MQ=255)
ctTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTGGCTGAACTg > 1:3412046/1‑69 (MQ=255)
ctTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTGGCTGAACTg > 1:3220571/1‑69 (MQ=255)
ttAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTGGCTGAACTgg > 1:2978395/1‑69 (MQ=255)
|
TTTGCGCATCGCTACCCGTCTCAACGACCAGCGCCCGGCAGAACTTCCCCCTCTTAACGTTCTGATTCAAATTAACATTAGTGATGAAAACAGTAAGTCCGGGATTCAACTGGCTGAACTGG > minE/1982406‑1982527
|
| 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
