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 |
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 | . | 84.6%
| 74.9
/ 12.3
| 26 | coding (143/1434 nt) | ygjI | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (3/1); new base . (11/11); total (14/12) |
| Fisher's exact test for biased strand distribution p-value = 5.98e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-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. |
TAACAACGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAA > W3110S.gb/3224964‑3225096
|
tAACAACGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAt > 1:610737/1‑69 (MQ=255)
aacaacGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtt > 1:3365265/1‑69 (MQ=255)
acGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAttttta > 1:1237654/1‑68 (MQ=255)
acGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAttttta > 1:868446/1‑68 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTc > 1:1082943/1‑69 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTc > 1:1838409/1‑69 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTc > 1:1936963/1‑69 (MQ=255)
taataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:222010/69‑1 (MQ=255)
aataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCt < 1:2734186/69‑1 (MQ=255)
ataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttttat > 1:1843898/1‑56 (MQ=255)
gAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTtctgtctg < 1:1630300/69‑1 (MQ=255)
gAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTACCTtc > 1:2816216/1‑63 (MQ=255)
ttGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGatcat > 1:1400227/1‑69 (MQ=255)
ttGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGatcat > 1:2112134/1‑69 (MQ=255)
tGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGatcat > 1:197717/1‑68 (MQ=255)
ggACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:1196286/41‑1 (MQ=255)
ggACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGatcat > 1:842383/1‑68 (MQ=255)
ggACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTc < 1:2565922/51‑1 (MQ=255)
ggACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTc < 1:1731107/51‑1 (MQ=255)
ggCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGtt > 1:1750520/1‑69 (MQ=255)
aCCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtct < 1:2187006/43‑1 (MQ=39)
aCCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtct < 1:2575373/43‑1 (MQ=39)
aCCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtct < 1:1496142/43‑1 (MQ=39)
aCCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCg > 1:879532/1‑55 (MQ=255)
gATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTta > 1:3624938/1‑69 (MQ=255)
tGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaa > 1:1516651/1‑68 (MQ=255)
tttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataaa < 1:215280/69‑1 (MQ=255)
tttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataaa < 1:153167/69‑1 (MQ=255)
cgcgACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCa < 1:2064521/69‑1 (MQ=255)
cgcgACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCa < 1:1880498/69‑1 (MQ=255)
gcgACGA‑TTTTTATTTTATTCACTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTc > 1:2485621/1‑67 (MQ=255)
acgaTTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGaa > 1:3104383/1‑69 (MQ=255)
|
TAACAACGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAA > W3110S.gb/3224964‑3225096
|
| 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
