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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,846,918 |
T→C |
36.8% |
V62A (GTT→GCT) |
htrL → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,846,918 | 0 | T | C | 36.8%
| 42.2
/ 61.0
| 57 | V62A (GTT→GCT) | htrL | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (12/24); new base C (8/13); total (20/37) |
| Fisher's exact test for biased strand distribution p-value = 7.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01 |
CTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATAT > W3110S.gb/3846850‑3846985
|
cTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTg < 1:4281341/71‑1 (MQ=255)
tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGaa > 1:4004173/1‑70 (MQ=255)
tGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAg > 1:4303805/1‑71 (MQ=255)
tGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCg > 1:436037/1‑70 (MQ=255)
ggCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGc > 1:296530/1‑70 (MQ=255)
ggCCGCACTTGAAAATGAGATCATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGc > 1:2665766/1‑70 (MQ=255)
gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCa < 1:4305073/70‑1 (MQ=255)
gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGc < 1:1129114/69‑1 (MQ=255)
gCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGc < 1:2469616/69‑1 (MQ=255)
ccGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGc < 1:1352281/68‑1 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCTATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa < 1:4758159/71‑1 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa < 1:984773/71‑1 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa < 1:3176042/71‑1 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGaa < 1:4042053/71‑1 (MQ=255)
aCTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGaa < 1:2990912/71‑1 (MQ=255)
cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAg > 1:2943715/1‑55 (MQ=255)
cTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa > 1:1622311/1‑70 (MQ=255)
ttGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGaa < 1:1510072/69‑1 (MQ=255)
tGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAAc > 1:4304784/1‑71 (MQ=255)
aaaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAAcc < 1:2690876/70‑1 (MQ=255)
aaaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAAcc < 1:2698598/70‑1 (MQ=255)
aaaTGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaa < 1:2980956/71‑1 (MQ=255)
ttattTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGGGATTCGCAACGGAAAACCAACAACGgttatc > 1:1225444/1‑71 (MQ=255)
tattTTCACTTCTCCCGATTTGAAACCAAGGGTTg > 1:3718567/1‑35 (MQ=255)
tattTTCACTTCTCCCGATTTGAAACCAAGGGTTg > 1:2982369/1‑35 (MQ=255)
tattTTCACTTCTCCCGATTTGAAACCAAGGGTTg > 1:4009458/1‑35 (MQ=255)
tattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac < 1:604408/60‑1 (MQ=255)
tattTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac < 1:925310/60‑1 (MQ=255)
attTTCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgt > 1:3384484/1‑71 (MQ=255)
attTTCACTTCTCACGATTTGAAACCAAGGGTTGAAGCGAtt > 1:779413/1‑42 (MQ=255)
ttttCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgtt < 1:688860/71‑1 (MQ=255)
ttttCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaac < 1:2453596/58‑1 (MQ=255)
ttCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat > 1:3034943/1‑71 (MQ=255)
tCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttatc > 1:4173437/1‑71 (MQ=255)
tCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat > 1:644194/1‑70 (MQ=255)
tCACTTCTCCCGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgttatcgttat > 1:147559/1‑70 (MQ=255)
cTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac < 1:4918136/52‑1 (MQ=255)
ttCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGc < 1:132197/37‑1 (MQ=255)
ttCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGgttatc < 1:4906490/61‑1 (MQ=255)
tcCCGATTTGAAACCAATGGTTGAAGCGATTCGCAACGGAAAACcaacaa < 1:1277130/50‑1 (MQ=255)
tcCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaacaa < 1:907040/50‑1 (MQ=255)
cccGATTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGgtt > 1:2405760/1‑54 (MQ=255)
ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaaa < 1:2318224/71‑1 (MQ=255)
ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaa < 1:3186439/69‑1 (MQ=255)
ccGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaa < 1:2314153/69‑1 (MQ=255)
cGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACcaac < 1:3840364/45‑1 (MQ=255)
aTTTGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACca < 1:4811373/41‑1 (MQ=255)
ttGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACcaac > 1:4728040/1‑41 (MQ=255)
tGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGaa < 1:4580484/70‑1 (MQ=255)
tGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGaa < 1:4503244/70‑1 (MQ=255)
tGAAACCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGaa < 1:4919402/70‑1 (MQ=255)
aaaCCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaa < 1:1836296/62‑1 (MQ=255)
aaaCCAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATaaa < 1:4475408/62‑1 (MQ=255)
cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGa < 1:3495054/71‑1 (MQ=255)
cAAGGGCTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGa < 1:3143469/71‑1 (MQ=255)
gggTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGatat < 1:446916/71‑1 (MQ=255)
gggTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGatat < 1:978484/71‑1 (MQ=255)
|
CTTTGAGCGTCTGGCCGCACTTGAAAATGAGATGATTATTTTCACTTCTCCCGATTTGAAACCAAGGGTTGAAGCGATTCGCAACGGAAAACCAACAACGGTTATCGTTATCGATATAAAAAAGAAATTTAGATAT > W3110S.gb/3846850‑3846985
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
