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 |
|
A27 F124 I0 R1
|
44 |
29.6 |
1159012 |
90.6% |
1050064 |
142.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
4,196,204 |
G→A |
100% |
intergenic (‑105/+128) |
thiC ← / ← rsd |
phosphomethylpyrimidine synthase/regulator of sigma D |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,196,204 | 0 | G | A | 93.6%
| 83.4
/ ‑2.0
| 32 | intergenic (‑105/+128) | thiC/rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (14/15); total (15/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAG > NC_000913/4196064‑4196339
|
gcgTGGTTCGCGGCGGGGTAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACGCTTGTTCCCTTcaca < 2:478789/143‑1 (MQ=255)
cgTTGTGCGCGGCGGGTCAGTTGTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAg < 1:460412/143‑1 (MQ=255)
gttggtCGCGGCGGGTCAGTTTGGTTGCGGACATAGCTCAGTCCAAAAAGTTAAGGACGTGGCGTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAgg < 1:278692/143‑1 (MQ=255)
ttCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGGGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTAtt > 1:332364/1‑143 (MQ=255)
tCAGTTTTGTTGCCGACATAGCTGATTCCAACAAGTTAAGGACGTTGCTTGTCAGACGACGGGTGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAg < 2:56551/143‑1 (MQ=255)
tCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAg > 1:172608/1‑143 (MQ=255)
tCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAg < 1:390286/143‑1 (MQ=255)
gCAGACATAGCTCATTCCAAAAGGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGAt > 1:135782/1‑143 (MQ=255)
cgcATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa < 1:384879/141‑1 (MQ=255)
tCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAAc > 1:226227/1‑143 (MQ=255)
cATTCCAAAAAGTGAAGGACGCGGGTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACCGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg < 1:254549/143‑1 (MQ=255)
aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCa > 2:352649/1‑143 (MQ=255)
aaaaaGTGAAGGACGGGGCGTGTCAGACGACGGAAGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCa < 1:156687/143‑1 (MQ=255)
ttAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGACCCCGACTAAACGGTCccagccagc > 2:307388/1‑142 (MQ=255)
aGGGCGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa < 1:538066/143‑1 (MQ=255)
tgacggcgCTTGTCAGACGACGGATGAAGCGAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCCTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCATCCAGTTAAg < 2:232460/136‑1 (MQ=255)
ggACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAg < 1:508282/143‑1 (MQ=255)
gACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCTCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAgg < 1:19634/143‑1 (MQ=255)
aCGTGGCTTGTCAGACGTCGGATCAAGCAAGAGACCATGTCCGCAGTGGCGTTGCGTTGGCAGATTAACTCTTGTTCCCTTCCCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGc < 2:85076/143‑1 (MQ=255)
cGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCa < 2:512482/143‑1 (MQ=255)
gTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACa > 1:203440/1‑143 (MQ=255)
tgggttGAAGCAAGAGACGGTCGCCGCAGGGGCGTTGGGATAGCAGATTAACTCATGTTCCCTTCACAGGTGTTATCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTa < 2:66469/138‑1 (MQ=255)
gcaTCGCCCCTGCGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTGCGCGGACCCCGACTAAACGGTCTCAGCCAGTTAAGCCACTCCGACAAGAAAGTCGCCCCGCCAACGGGGCa > 2:294738/3‑143 (MQ=255)
aTCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt < 1:452207/143‑1 (MQ=255)
aTCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt > 1:400915/1‑143 (MQ=255)
ggggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTaaa < 1:352649/143‑1 (MQ=255)
atgcgatAGCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgc > 2:552894/1‑143 (MQ=255)
atgcgatAGCAGATTAACTCTTGTTCCCTTAACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgc > 1:530531/1‑143 (MQ=255)
gCAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGACTAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTACCAg > 2:509912/1‑143 (MQ=255)
cAGATTAACTCTTGTTCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAgc > 1:180493/1‑143 (MQ=255)
ttAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGAAAATGGGGCATCGAATGTAAATTACGCGTTAACAGCGCAg > 2:559433/1‑143 (MQ=255)
ttCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa < 1:500574/143‑1 (MQ=255)
tCCCTTCACAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAg > 1:492880/1‑143 (MQ=255)
|
GCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAG > NC_000913/4196064‑4196339
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
