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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,225,032 |
Δ1 bp |
100% |
coding (143/1434 nt) |
ygjI → |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,225,032 | 0 | T | . | 76.7%
| 63.9
/ 25.9
| 30 | coding (143/1434 nt) | ygjI | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (7/0); new base . (9/14); total (16/14) |
| Fisher's exact test for biased strand distribution p-value = 7.31e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.22e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAA > W3110S.gb/3224975‑3225088
|
tCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTc < 1:1517994/71‑1 (MQ=255)
taataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCt > 1:3155946/1‑70 (MQ=255)
aataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:466495/1‑71 (MQ=255)
ataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:2364588/1‑70 (MQ=255)
aataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTttttatttta > 1:1467561/1‑61 (MQ=255)
aataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTttttatttta > 1:290221/1‑61 (MQ=255)
aataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTttttatttta > 1:2842250/1‑61 (MQ=255)
aataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTttttatttta > 1:3238173/1‑61 (MQ=255)
aataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTttttatttta > 1:707618/1‑61 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAttt > 1:44722/1‑48 (MQ=255)
gAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGat > 1:2456490/1‑70 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAg < 1:3009981/71‑1 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAg < 1:3005692/71‑1 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAg < 1:3506964/71‑1 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAg < 1:3597755/71‑1 (MQ=255)
cTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGaa > 1:208478/1‑71 (MQ=255)
tGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:330470/44‑1 (MQ=255)
tGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:1759760/44‑1 (MQ=255)
tGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:2850025/44‑1 (MQ=255)
gCCTCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:1762879/42‑1 (MQ=255)
tCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:808891/39‑1 (MQ=39)
tCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:2673240/39‑1 (MQ=39)
tCGGCACCGATGTTTTTCCTCGCGACGA‑Tttttatttta < 1:850935/39‑1 (MQ=39)
tCGGCACCGATGTATTTCCTCGCGACGA‑Tttttatttta < 1:1474015/39‑1 (MQ=25)
ggCACCGATGTTTTTCCTCGCGACGATTttttatt > 1:2959623/1‑35 (MQ=255)
ggCACCGATGTTTTTCCTCGCGACGATTTtttattttat > 1:2812889/1‑39 (MQ=255)
ggCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:2348217/1‑45 (MQ=255)
ccGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAAttt < 1:239687/62‑1 (MQ=255)
aTGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaat < 1:991063/71‑1 (MQ=255)
tGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaata < 1:1108401/71‑1 (MQ=255)
tGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaata < 1:1487203/71‑1 (MQ=255)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtct < 1:2507771/36‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtct < 1:2290109/36‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtct < 1:2233139/36‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataaa < 1:2197058/71‑1 (MQ=255)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataaa < 1:2161410/71‑1 (MQ=255)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataa > 1:3173200/1‑70 (MQ=255)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataa > 1:2226798/1‑70 (MQ=255)
tttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATaaaa > 1:3136126/1‑70 (MQ=255)
|
TCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAA > W3110S.gb/3224975‑3225088
|
| 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
