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 |
|
A17 F109 I0 R1
|
32 |
27.2 |
584098 |
96.5% |
563654 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,440,007 |
Δ1 bp |
100% |
coding (34/201 nt) |
cspA ← |
cold shock protein CspA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,440,007 | 0 | C | . | 93.4%
| 113.6
/ 0.8
| 30 | coding (34/201 nt) | cspA | cold shock protein CspA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base . (10/18); minor base T (1/0); total (11/19) |
| Fisher's exact test for biased strand distribution p-value = 3.79e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.91e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATA > CP000730/1439878‑1440141
|
cGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAAcc > 1:264062/1‑140 (MQ=255)
ttCAACTACTTCAATCTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAttt < 2:64912/140‑1 (MQ=255)
ttCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAttt < 1:235190/140‑1 (MQ=255)
ttCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAttt < 1:268745/140‑1 (MQ=255)
ctTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAc < 2:250306/140‑1 (MQ=255)
ctTCAAACTCAACAGCTTGACCTTCTACTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTATAc > 2:174279/1‑140 (MQ=255)
aaaaaTCAACAGCTTGACATTATTCTAATGATTTATAATCATCTTGGTTAATTGCTGAAGATTTAAAGATTACGTTATTTTATCCTTCAACTTCGAGAAAGACGAATCCTTTTT‑ACGGTTAAAACATTGAACTGTACGtt > 2:91577/2‑140 (MQ=255)
aCTCAACAGCTTGATCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGtt < 1:277014/140‑1 (MQ=255)
actttctccTAATTGTTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAATCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGaat < 2:217799/137‑2 (MQ=38)
aCCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGaaa < 1:86997/140‑1 (MQ=255)
cttcttCTATTGATTTGTAACCATCTTGGTTAATCGCTGAAAAGTGTACGATTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAcc < 2:148946/140‑1 (MQ=39)
cttcgtCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAcc < 2:242487/140‑1 (MQ=255)
cttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTcc > 1:2056/1‑140 (MQ=255)
tAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGa < 2:264062/140‑1 (MQ=255)
aTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACt < 2:2056/140‑1 (MQ=255)
gATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa < 2:157570/140‑1 (MQ=255)
aaCCATCTTGGTTAATTGCCGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcat < 2:262714/140‑1 (MQ=255)
ccATCTTGGCTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCGTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc > 2:186766/1‑140 (MQ=255)
ggTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGc < 1:38995/140‑1 (MQ=255)
tGAAAAATGTCCGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATGC‑ATGTGTCTATTGAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCat < 1:211354/140‑1 (MQ=255)
tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCAAAAACAAAACTTCATTCAATATGCTTATTCCCat > 2:111509/1‑140 (MQ=255)
gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑ATCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaa > 1:88071/1‑140 (MQ=255)
cGTCATTTTCTCCTTCAACTTCGATAAATCCTAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg < 2:51896/140‑1 (MQ=255)
aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCaaa > 2:284049/1‑140 (MQ=255)
aaCTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATACGCATATTACAAAAAATACATGCAAATTTCACTCAAat < 1:186766/140‑1 (MQ=255)
cTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTATCTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAatat < 1:65557/140‑1 (MQ=255)
tAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGAAAATTTCACTCAAATATTCTTTg > 1:114879/1‑140 (MQ=255)
ccGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAata < 1:91577/140‑1 (MQ=255)
aaTCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAGTCTGAAACCTCCAAGACTAATATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg > 2:190533/1‑140 (MQ=255)
cttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaata > 1:72024/2‑140 (MQ=255)
|
CGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATA > CP000730/1439878‑1440141
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
