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 |
1,109,964 |
G→A |
100% |
C185C (TGC→TGT) |
mdoC ← |
membrane protein required for modification of periplasmic glucan |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,109,964 | 0 | G | A | 89.7%
| 74.2
/ 2.0
| 29 | C185C (TGC→TGT) | mdoC | membrane protein required for modification of periplasmic glucan |
| Reads supporting (aligned to +/- strand): ref base G (3/0); new base A (14/12); total (17/12) |
| Fisher's exact test for biased strand distribution p-value = 2.46e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACTCAGAATGGGCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGGCATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTAAAT > W3110S.gb/1109901‑1110031
|
aCTCAGAATGGGCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaa > 1:1130721/1‑70 (MQ=255)
cTCAGAATGGGCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaaaa < 1:1406345/71‑1 (MQ=255)
cTCAGAATGGGCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaaaa < 1:2744982/71‑1 (MQ=255)
tGGGCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGGCATAAAAAAATCAcc > 1:223422/1‑71 (MQ=255)
ggCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaa > 1:981132/1‑60 (MQ=255)
ggCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaa > 1:1046097/1‑60 (MQ=255)
ggCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaa > 1:899379/1‑60 (MQ=255)
gATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGt < 1:678578/71‑1 (MQ=255)
tACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGttt > 1:3569026/1‑71 (MQ=255)
tACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGttt > 1:1443385/1‑71 (MQ=255)
cacaATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATaaaaaaa > 1:2525387/1‑56 (MQ=255)
caATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGtttt < 1:1991795/68‑1 (MQ=255)
caATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGtttt < 1:3045083/68‑1 (MQ=255)
caATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGtttt < 1:1437656/68‑1 (MQ=255)
caATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGtttt < 1:2395103/68‑1 (MQ=255)
caATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGtttt < 1:2650328/68‑1 (MQ=255)
aTAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGGCATAAAAAAATCACCGATAGTTTTACCAt > 1:2626069/1‑71 (MQ=255)
gTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGt > 1:1611871/1‑54 (MQ=255)
gTTCTTCTTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGt > 1:2167445/1‑54 (MQ=255)
tcttctTATTACCGCATAACCGATGCCGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAAttttt > 1:674573/1‑71 (MQ=255)
cATAACCGATGCCGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTAt > 1:2554754/1‑69 (MQ=255)
tAACCGATGCCGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTc < 1:146429/60‑1 (MQ=255)
aCCGATGCCGAGGCATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAAt > 1:1217967/1‑71 (MQ=255)
aCCGATGCCGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTAtt > 1:1377930/1‑57 (MQ=255)
aCCGATGCCGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAAt > 1:3607237/1‑71 (MQ=255)
aCCGATGCCGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAAt > 1:1680281/1‑71 (MQ=255)
ccGAGACATAAAAATATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTaa < 1:2389447/71‑1 (MQ=255)
ccGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTaa < 1:1806980/71‑1 (MQ=255)
ccGAGACATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTaa < 1:3633732/71‑1 (MQ=255)
gagaCATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTAAat > 1:2100308/1‑71 (MQ=255)
gagaCATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTAAat > 1:3569761/1‑71 (MQ=255)
gagaCATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTAAat > 1:1726776/1‑71 (MQ=255)
|
ACTCAGAATGGGCGGATACACAATAAAAATCGTTCTTCTTATTACCGCATAACCGATGCCGAGGCATAAAAAAATCACCGATAGTTTTACCATCGAGAATTTTTTATTCGTTTTATCAGAATTTTCTAAAT > W3110S.gb/1109901‑1110031
|
| 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
