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 |
|
A13 F191 I0 R1
|
49 |
68.0 |
1456600 |
97.2% |
1415815 |
140.0 |
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 | . | 97.4%
| 160.0
/ ‑2.0
| 38 | coding (34/201 nt) | cspA | cold shock protein CspA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base . (13/24); minor base T (0/1); total (13/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.86e-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. |
GCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT > CP000730/1439873‑1440140
|
gctgTCGCCTTCAACTACTTTAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGtt < 1:89443/137‑1 (MQ=255)
gacctatacaactTCATACGCAACAGCTTGACCTTCTTCTAATGCGTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACTAATTCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCa < 2:74247/130‑1 (MQ=255)
cacTTCGACTAGTTCAAACTCTCCGGCTTGTCCTTCTTCTATTGATTTGTAACCCTCTTGGTTAATTGCTGAAAAATGTTCGAACACGTCATTTTCTCCTTCAACTTCGTTAAAGCCGAATCCTTTTT‑AGCGTTAAACCa < 2:74271/138‑1 (MQ=255)
cTTTAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAtt < 2:119421/140‑1 (MQ=255)
cTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAtt < 2:666980/140‑1 (MQ=255)
cTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAtt < 2:666981/140‑1 (MQ=255)
ctactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAACACGTCATTTTCTCCTTCAACTTCGATCAAGCCTAATCCTTTTT‑AGCGTTAAACCATTTAACTg < 1:646418/140‑1 (MQ=255)
tcccatttcgtcAGGTTGACCTTTGTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAcc < 2:147713/129‑1 (MQ=255)
cTCAACAGCTTGACCTTCTTCTGCGAAGTGGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGttt > 1:720294/1‑140 (MQ=255)
cAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCa > 1:36271/1‑140 (MQ=255)
aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAACCGAATCCTTTTT‑GGCGTTAAACCAGTTAACTGTACCTTGTTTCATAAt > 1:132745/1‑140 (MQ=38)
aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTAATTTTTTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGTGTTAAAACTTTTAACTGTACCTTTTTTCATTAt > 1:22723/1‑140 (MQ=38)
gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc < 1:136010/140‑1 (MQ=255)
cTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt < 2:356270/140‑1 (MQ=255)
tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa > 2:412397/1‑140 (MQ=255)
tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa > 2:412556/1‑140 (MQ=255)
aaTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAc < 2:136323/140‑1 (MQ=255)
ccATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc > 1:650578/1‑140 (MQ=255)
cTTGGTTAATTGCTGAAAAATGTTCGAATACGTCATTTTCTCCTTCAACTTCGATATAGCCGATTCCTTTTT‑AGCGTTAATCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAata < 1:3358/140‑1 (MQ=255)
cTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAata < 1:603889/140‑1 (MQ=255)
aaTTGCTGAAAAAGGTTCGGATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTGCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAt < 1:487978/140‑1 (MQ=255)
aaaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACGTCCACAACTAAAATTCATTCAATATGCTTATTCGCATAtt > 1:377028/1‑140 (MQ=255)
aaaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCACTTTT‑ACCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGACACCTCCACGCCTAAAATTCATTCAATATCCTTATTCGCACAtt > 2:351020/1‑140 (MQ=255)
aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAc < 1:54905/140‑1 (MQ=255)
tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATACTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaa < 2:374199/140‑1 (MQ=255)
cGAATACGTCATTTTCTCCTTCAATTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTGTTCGCATATTACaaaaaa > 1:462636/1‑140 (MQ=255)
ccTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTAACt > 1:255006/1‑140 (MQ=255)
tccaCTTCGATAATGCCGATTTCTTTTT‑AGCGTTTAATCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTCACTCGCATATTACAAAAAAGACATGCAAATTTCACTCaa < 1:472758/137‑1 (MQ=255)
cAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa < 1:368790/140‑1 (MQ=255)
gATACACCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGACACCTCAAAGACTAAAATTCATCCAATATGCTTATTAGAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCtt < 2:367138/140‑1 (MQ=255)
gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTACCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATCCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCACATTTCACTCAAATATTcgt < 2:718764/140‑3 (MQ=255)
gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt > 1:239249/1‑140 (MQ=255)
gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTCAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt < 2:432743/140‑1 (MQ=255)
tAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg < 2:256351/140‑1 (MQ=255)
cGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat < 2:48729/140‑1 (MQ=255)
aaTCCTTTTT‑AGCGTCAAACCATTTAACTGTACCTTGTTTCATAATCGGAATCCCCCAAGACTAAAATTCATTCAATATGCTTATTCGCATAGTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg < 2:139253/140‑1 (MQ=255)
aattcttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg < 2:33789/135‑1 (MQ=255)
ccTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGAaat > 2:440255/1‑140 (MQ=255)
|
GCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT > CP000730/1439873‑1440140
|
| 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
