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 |
|
A15 F58 I0 R3
|
247 |
66.2 |
2815674 |
94.9% |
2672074 |
126.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP006881 |
3,725,205:1 |
+T |
100% |
intergenic (‑37/‑492) |
U712_19205 ← / → U712_19210 |
Uncharacterized protein ywcI/Minor extracellular protease vpr |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP006881 | 3,725,205 | 1 | . | T | 78.1%
| 73.1
/ 19.0
| 32 | intergenic (‑37/‑492) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base . (2/5); new base T (18/6); total (21/11) |
| Fisher's exact test for biased strand distribution p-value = 6.65e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TGAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑TT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCA > CP006881/3725068‑3725331
|
tGAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACCAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑Gc‑cg > 1:110479/1‑138 (MQ=255)
aaTAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACCCCCGTAAAGATACAAGCAAACGTTTCATAGATAAACATCCCTCCGCTTCTTTTTGGCAGGCC‑GC‑C‑tt‑tttag > 2:209018/1‑135 (MQ=255)
gACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTTGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGcc > 7:216067/1‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACACGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGt > 6:330605/2‑139 (MQ=255)
gtcAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATCCAAGCAAACGTATCATAGAAAAACAACCCTCCGCGTCTATTTGGCATGCACGC‑T‑GT‑TT‑A‑TCACCCAGtttt > 4:212853/3‑139 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGtttt > 8:297151/1‑139 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGttt > 4:189360/1‑138 (MQ=255)
cTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGcccg < 7:297151/138‑2 (MQ=255)
cGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCGGCCGCAGcccgcaaga > 5:154530/1‑132 (MQ=255)
cGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGGTTTCTCAGCCGCAGcccgcaaga > 5:100925/1‑132 (MQ=255)
cccAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTTGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGc > 1:181369/1‑139 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtt > 5:88673/1‑139 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CGTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCCGCCCGCCAGAAAAGCCGGCCGAtt > 5:197534/1‑139 (MQ=255)
caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttcttt > 7:21704/1‑139 (MQ=255)
aaaGACCATCCACACCCGTAAAGATACAAGCAATCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCTGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttctttt > 5:151715/1‑137 (MQ=255)
aGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCg > 4:66011/1‑139 (MQ=255)
aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTCTAGCAAAc > 3:122815/1‑139 (MQ=255)
cccGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGc > 8:111613/1‑139 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc > 2:221533/1‑137 (MQ=255)
aaGAAACAACAAAACGTTTAATACAAAAACACCCCTCCGCTTCTTTTGGCCAGGCA‑GC‑CTTT‑TT‑C‑GCCCCCCG‑TTTCTCCCCCCCCCCCCCCAACAACCCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 1:75882/139‑1 (MQ=255)
aGATACACGCAAACGTTTCATAGAAAAACAACCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑CCAGCCCGTTTTCTCAGCCGCAGCCCCCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:4564/139‑1 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCCCAAACTATCGGCTCTAGCaaaa > 4:158311/1‑138 (MQ=255)
gCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GCGT‑TT‑TT‑A‑GCAGCCCGGTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTATCGGCTCTAGCAAAACTCAt > 5:279858/1‑139 (MQ=255)
cAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATg < 7:111613/139‑1 (MQ=255)
ccggttCATCTAAAAACATCCCTCCGCTTCTTTTGGCCCGCCC‑GC‑C‑TTGTT‑C‑GCCCCCCGTTTGCTCCCCCGCAGCCCCAAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 4:149587/135‑1 (MQ=255)
agttttAATATAAAAACATCCCTCGGCTTTTTTTTGCCCGGAA‑GC‑CTTT‑TT‑T‑GCAGCCCGTTTTCTCCCCCCCCCCCCCAACTAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 6:88673/136‑1 (MQ=255)
aCGTTTCATCTAAAACCATCCCTCCGCTTCTTTTTGGCAGGCA‑GCAT‑TT‑TT‑A‑GCAGCCGGTTTTCTCCGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 7:44408/139‑1 (MQ=255)
aCGTTTAATAGAAAAAAATCCCTCCGCTTCTTTTTGGCTGGCC‑GC‑C‑TT‑TTAA‑GCCGCCGGTTTTCTCGGCCGCCGCCCGCATGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 6:154530/139‑1 (MQ=255)
aCGTTTAATAAAAAACCATCCACCCTCTTATTTTTAGCAGCCA‑GCTT‑TT‑TT‑A‑CCAGCCGTTTTACTCCGCCCCCCCCCGCAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 5:75731/139‑1 (MQ=255)
aCGTTCCATACAAAACCACCCCACCCCTTATTTTTGGCCGCCC‑CC‑C‑TT‑TA‑ACGCACCCCGTTTACCCCCCCCCTCCCCCCATCAAACCACGGCCGATTGCTTTTCTCGCAAACAAGCGGCTCTAGCAAAACTCATGAct < 7:189506/139‑1 (MQ=255)
aCGATTCATACAAAAACATCCCACCGCTTCTTTTTGGCCGGCA‑CC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCACCCCGCAAGAAACCACGGCCGATTTCTTTTCTCCCAAACTAGCGGCTCTAGCAAAACTCATGAct < 3:176101/139‑1 (MQ=255)
ttCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCATCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAATCATGCCTCGAt > 1:204671/1‑139 (MQ=255)
ccGCTTCTTTTTGGCAGGCA‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACGCTATGATAGACCGTGGAAagag > 7:247690/1‑138 (MQ=255)
ggcaggca‑GC‑CTTT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTca > 5:237982/1‑138 (MQ=255)
|
TGAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCA‑GC‑C‑TT‑TT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCA > CP006881/3725068‑3725331
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
