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 |
4,457,853 |
Δ1 bp |
coding (13/552 nt) |
yjgA ← |
DUF615 domain‑containing protein YjgA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,457,851 | 0 | G | . | 97.4%
| 151.2
/ ‑2.9
| 38 | coding (15/552 nt) | yjgA | DUF615 domain‑containing protein YjgA |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base . (22/15); minor base T (1/0); total (23/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTCACTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTCGGGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACGGTT > NC_000913/4457772‑4457926
|
tttCACTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTCgg > 2:852279/1‑81 (MQ=255)
cACTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCTCCGGGAACGTCGTCGAGCCAGTCTTCggctg > 2:852264/1‑78 (MQ=255)
cACTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTCggct < 1:852224/80‑3 (MQ=255)
cTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑Ggctgct < 1:852225/81‑1 (MQ=255)
cTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑Ggctgct < 2:852225/81‑1 (MQ=255)
ttACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCtt < 1:852227/79‑1 (MQ=255)
tACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAg < 2:852227/80‑1 (MQ=255)
aCTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGt > 2:852284/1‑80 (MQ=255)
cTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCa > 1:852277/1‑81 (MQ=255)
cTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCa > 1:852292/1‑81 (MQ=255)
gACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCAtc > 1:852282/1‑81 (MQ=255)
cccAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCAtctc < 1:852229/81‑1 (MQ=255)
cAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAg > 2:852287/1‑81 (MQ=255)
gATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGc < 1:852230/81‑1 (MQ=255)
tttCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCt > 1:852272/1‑80 (MQ=255)
aTCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTaaa > 2:852302/1‑80 (MQ=255)
cgtcttcgtcttCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTaaaaa > 2:852305/1‑80 (MQ=255)
cgtcttcgATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAagag < 1:852231/79‑1 (MQ=255)
cgtcttcgATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGc > 1:852289/1‑81 (MQ=255)
cttcgATGTCATCACCGGGAACGTCGTCGAGCCAGTCTT‑TGGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTaa > 1:852293/1‑81 (MQ=255)
tcgATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTATAAAAAGAGGCTAATg > 2:852286/1‑81 (MQ=255)
cgATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATg < 2:852231/80‑1 (MQ=255)
atcaCCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAg < 1:852233/80‑1 (MQ=255)
atcaCCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGt > 1:852290/1‑81 (MQ=255)
aCCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGtt > 2:852295/1‑79 (MQ=255)
aCCGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTa < 1:852234/80‑1 (MQ=255)
ccGGGAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAg < 2:852234/81‑1 (MQ=255)
gggAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGAt > 1:852284/1‑81 (MQ=255)
gggAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGAt < 1:852236/81‑1 (MQ=255)
gAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATgc < 2:852236/81‑1 (MQ=255)
gAACGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATgc > 2:852298/1‑81 (MQ=255)
aCGTCGTCGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATgcg > 1:852286/1‑80 (MQ=255)
gtcgtcGAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCAc > 1:852295/1‑81 (MQ=255)
gtcgAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTg > 2:852301/1‑80 (MQ=255)
tcgAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGa > 1:852294/1‑80 (MQ=255)
gAGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGaaa > 2:852299/1‑80 (MQ=255)
aGCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGaaaaa < 2:852237/81‑1 (MQ=255)
gCCAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAAc > 1:852304/1‑81 (MQ=255)
ccAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACg < 1:852239/81‑1 (MQ=255)
ccAGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACg < 1:852240/81‑1 (MQ=255)
aGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACGGt > 1:852307/1‑81 (MQ=255)
aGTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACGGt > 2:852304/1‑81 (MQ=255)
gTCTTC‑GGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACGGtt < 2:852240/81‑1 (MQ=255)
|
TTTCACTTTTACTGACCCAGATAATTTCATCGTCTTCGTCTTCGATGTCATCACCGGGAACGTCGTCGAGCCAGTCTTCGGGCTGCTTAGTCATCTCAGGCTCCTTAAAAAAAGAGGCTAATGTTACCAGTTAAGATGCGCACTGAAAAACGGTT > NC_000913/4457772‑4457926
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
