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 |
393,168 |
T→C |
79.2% |
G310G (GGT→GGC) |
yaiU → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 393,168 | 0 | T | C | 79.2%
| 102.0
/ 22.0
| 48 | G310G (GGT→GGC) | yaiU | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (7/3); new base C (20/18); total (27/21) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01 |
TTTGTTGATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTAC > W3110S.gb/393103‑393228
|
tttGTTGATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACt < 1:3215709/69‑1 (MQ=255)
ggTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGAc < 1:208402/69‑1 (MQ=255)
gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGAc > 1:1271515/1‑68 (MQ=255)
gTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGAc > 1:3405166/1‑68 (MQ=255)
ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt > 1:106493/1‑60 (MQ=255)
ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt > 1:320846/1‑60 (MQ=255)
ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAg < 1:2891155/68‑1 (MQ=255)
ttGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAg < 1:2886757/68‑1 (MQ=255)
aCTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGtt > 1:1181937/1‑53 (MQ=255)
ctctCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACgg > 1:339954/1‑57 (MQ=255)
ctctCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACgg > 1:237870/1‑57 (MQ=255)
ctctCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACgg > 1:921658/1‑57 (MQ=255)
tctcACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTcc > 1:274120/1‑69 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGtt > 1:1691025/1‑47 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACg > 1:557164/1‑69 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACg > 1:1555968/1‑69 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACt > 1:2076275/1‑41 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACt > 1:703681/1‑41 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACt > 1:2308280/1‑41 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACt > 1:605813/1‑41 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGa < 1:374616/67‑1 (MQ=255)
aCTTCAACAACGACCTGTCTGCAACCATGAG‑AACGGCACt > 1:414637/1‑40 (MQ=255)
ttCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGc < 1:212127/68‑1 (MQ=255)
ttCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGc < 1:3174651/68‑1 (MQ=255)
ttCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGc < 1:2941778/68‑1 (MQ=255)
ttCAACAACGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCt < 1:2158888/69‑1 (MQ=255)
acaacGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg < 1:3360922/68‑1 (MQ=255)
aacGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGAc > 1:1132137/1‑42 (MQ=255)
aacGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGAc > 1:79814/1‑42 (MQ=255)
aacGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGAc < 1:2938753/42‑1 (MQ=255)
aacGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGAc < 1:1578683/42‑1 (MQ=255)
cGACCTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTgg < 1:1878186/64‑1 (MQ=255)
ccTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTcc < 1:3063524/52‑1 (MQ=255)
ccTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTcc < 1:2416815/52‑1 (MQ=255)
cTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGt > 1:3118485/1‑69 (MQ=255)
cTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGt > 1:1164445/1‑69 (MQ=255)
cTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGt > 1:2491374/1‑69 (MQ=255)
cTGTCTGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGt > 1:1552254/1‑69 (MQ=255)
tGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGaa > 1:2961862/1‑69 (MQ=255)
tGCAACCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGaa > 1:2075515/1‑69 (MQ=255)
aCCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGc < 1:1634737/68‑1 (MQ=255)
aCCATGAGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGc < 1:2490666/68‑1 (MQ=255)
aGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt > 1:753970/1‑66 (MQ=255)
aGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGt > 1:2676754/1‑66 (MQ=255)
aGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTAc < 1:1954013/69‑1 (MQ=255)
aGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTAc < 1:1836231/69‑1 (MQ=255)
aGCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTAc < 1:589810/69‑1 (MQ=255)
gCAACGGCACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGc < 1:1451574/61‑1 (MQ=255)
|
TTTGTTGATGGTAGCTTGAGCTACTCTCACTTCAACAACGACCTGTCTGCAACCATGAGCAACGGTACTTACGTTGACGGTAGCACCAACTCCGACGCTTGGGGCTTCGGTTTGAAAGCCGGTTAC > W3110S.gb/393103‑393228
|
| 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
