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 |
3,060,772 |
(T)8→9 |
intergenic (+126/‑78) |
argP → / → scpA |
DNA‑binding transcriptional dual regulator ArgP/methylmalonyl‑CoA mutase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,060,764 | 1 | . | T | 96.7%
| 103.2
/ ‑3.2
| 30 | intergenic (+118/‑86) | argP/scpA | DNA‑binding transcriptional dual regulator ArgP/methylmalonyl‑CoA mutase |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (15/14); total (15/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
CCTCACTTCTTTTTGTATTCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCA‑‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGTTTTAC > NC_000913/3060686‑3060839
|
ccTCACTTCTTTTTGTATTCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCA‑‑tt > 1:503833/1‑81 (MQ=255)
aCTTCTTTTTGTATTCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCA‑‑tttt < 1:503800/79‑1 (MQ=255)
tttGTATTCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCA‑‑tttttttttg < 2:503800/78‑3 (MQ=255)
ttCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGAc < 1:503802/80‑1 (MQ=255)
ttCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGAc > 2:503830/1‑80 (MQ=255)
ccTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACaa < 2:503802/80‑1 (MQ=255)
cTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAAc > 1:503845/1‑81 (MQ=255)
tGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAAcc > 2:503828/1‑80 (MQ=255)
aaTCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCAc < 2:503803/81‑1 (MQ=255)
tcacatcacaAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGt < 2:503804/81‑1 (MQ=255)
cacatcacaAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCATTTTTTTTTTGCTGGCGACAAACCCACg > 2:503839/1‑80 (MQ=255)
cacatcacaAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGt > 2:503831/1‑80 (MQ=255)
acatcacaAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTaa < 1:503806/81‑1 (MQ=255)
acaAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAg < 2:503806/80‑1 (MQ=255)
aaaaTAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTc < 1:503808/81‑1 (MQ=255)
gACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCA‑‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAg < 1:503809/81‑1 (MQ=255)
aaaTCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGgc < 1:503810/81‑1 (MQ=255)
aTCTCAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGgcgc < 2:503810/81‑1 (MQ=255)
tcAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCaaa > 1:503843/1‑81 (MQ=255)
cAGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCaaa > 2:503833/1‑80 (MQ=255)
aGGCGGCAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCaa < 1:503812/78‑1 (MQ=255)
gcAAAAAACGACGTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTc < 1:503813/81‑1 (MQ=255)
acgacgTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGa > 1:503836/1‑81 (MQ=255)
cgacgTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGAt > 2:503836/1‑81 (MQ=255)
gacgTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGAtt > 2:503841/1‑81 (MQ=255)
gacgTCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGAtt > 2:503846/1‑81 (MQ=255)
tCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGt < 2:503813/81‑1 (MQ=255)
tCTGAATGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGt > 2:503838/1‑81 (MQ=255)
aaTGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGtttt < 2:503815/80‑1 (MQ=255)
aaTGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGttt < 1:503817/79‑1 (MQ=255)
aaTGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGTTTTa > 1:503844/1‑81 (MQ=255)
aaTGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGTTTTa > 2:503848/1‑81 (MQ=255)
aTGCAT‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGTTTTAc > 1:503838/1‑81 (MQ=255)
|
CCTCACTTCTTTTTGTATTCCTTGAATCACATCACAAAATAGACAAATCTCAGGCGGCAAAAAACGACGTCTGAATGCA‑‑TTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCACCGTAGGCGCAAATACCCTCATTTTGATTGCGTTTTAC > NC_000913/3060686‑3060839
|
| 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
