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 F1 I1 R1
|
690 |
31.8 |
1836723 |
97.1% |
1783458 |
80.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,079,659 |
Δ1 bp |
coding (1977/1992 nt) |
tktA ← |
transketolase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,079,656 | 0 | T | . | 96.2%
| 99.3
/ ‑3.2
| 26 | coding (1980/1992 nt) | tktA | transketolase 1 |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base . (15/10); total (16/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCTTTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGATTCAC > NC_000913/3079578‑3079729
|
ccGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCttt > 1:507839/1‑81 (MQ=255)
ccGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCttt > 2:507847/1‑81 (MQ=255)
aCGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTc > 1:507838/1‑81 (MQ=255)
aCGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTc < 2:507816/81‑1 (MQ=255)
cATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGcaa > 1:507854/1‑80 (MQ=255)
aaGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGtt < 1:507818/81‑1 (MQ=255)
gTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTAt > 1:507869/1‑80 (MQ=255)
taataaAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCa < 2:507818/81‑1 (MQ=255)
aaaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTg > 2:507877/1‑80 (MQ=255)
aaaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTg > 2:507844/1‑80 (MQ=255)
aaaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTT‑TTTTGCTTTCGCAACAACGTTATCAACAGTg > 2:507852/1‑80 (MQ=255)
aaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGaa < 1:507820/81‑1 (MQ=255)
gTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGcc > 2:507820/1‑81 (MQ=255)
gAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAActc > 2:507875/1‑81 (MQ=255)
aGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCtt < 1:507822/81‑1 (MQ=255)
cGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAATAACGTTATCAACAGTGAAGCCGAACTCTTc > 2:507850/1‑80 (MQ=255)
gACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCa > 1:507850/1‑80 (MQ=255)
aCCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCaaa > 1:507859/1‑81 (MQ=255)
cTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAAca < 2:507822/81‑1 (MQ=255)
tttACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAAcagc < 2:507823/80‑1 (MQ=255)
acacGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACagcagc < 2:507824/77‑1 (MQ=255)
aCCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGct > 2:507859/1‑81 (MQ=255)
ccGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGctct > 1:507875/1‑81 (MQ=255)
aaaTGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGcc > 2:507866/1‑81 (MQ=255)
gCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAg > 1:507872/1‑81 (MQ=255)
tAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAg > 1:507857/1‑79 (MQ=255)
aTTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGa < 2:507825/81‑1 (MQ=255)
agcagTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGATTCAc < 2:507826/81‑1 (MQ=255)
|
CCGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCTTTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGATTCAC > NC_000913/3079578‑3079729
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
