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 |
|
A20 F53 I0 R4
|
206 |
63.7 |
2487030 |
95.4% |
2372626 |
127.0 |
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 | 85.0%
| 82.0
/ 14.3
| 40 | intergenic (‑37/‑492) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base . (2/4); new base T (24/5); total (31/9) |
| Fisher's exact test for biased strand distribution p-value = 2.73e-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. |
TGAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑T‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAA > CP006881/3725068‑3725315
|
tGAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑t > 2:21001/1‑139 (MQ=255)
gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCGTTTTGGCAGgccgc‑cgt > 5:236256/1‑137 (MQ=255)
aGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTATCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑t‑tt > 7:30215/1‑139 (MQ=255)
accgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑T‑GCAGccc > 3:307744/4‑139 (MQ=255)
accgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TGTTT‑A‑GCAGccc > 3:265042/4‑139 (MQ=255)
accgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCGTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCATccc > 8:246969/4‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCCGCCCGt > 6:108247/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGt > 1:10077/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGt > 4:230315/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CGT‑TTT‑A‑GCAGCCCGt > 3:291795/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTAGGGCAGGCAGC‑C‑T‑TTT‑ATGCAGCCCGt > 4:297440/2‑139 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGCCCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CGT‑TTT‑A‑GCAGCCCGtttt > 1:6945/1‑139 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGgttt > 5:262056/1‑139 (MQ=255)
ccGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTGTTTTTTGGAGGCAGC‑CGA‑TTT‑A‑GCATCGCGGTTTATCAg > 3:4654/1‑139 (MQ=255)
tCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGcccgc > 8:178287/1‑134 (MQ=255)
gTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGa < 7:178287/139‑1 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGcccg < 2:36034/120‑2 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGcccg > 1:36034/1‑119 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGGCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGGGTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtg > 3:289871/1‑138 (MQ=255)
aGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCAGC‑CTT‑TTT‑A‑GCCGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCg > 7:201611/1‑139 (MQ=255)
aGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATGTCTTTTCTCg > 8:141885/1‑139 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTATCGCAAACTAGCGGGTCTa > 4:65951/1‑139 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGctc > 1:165876/1‑137 (MQ=255)
aGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGAGTCTTTTTGGCTGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 8:67399/139‑1 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGCGTTGATTTGTCGGCAACTAGCCGGGGTAGCaaaa > 1:132172/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCGC‑CGT‑TTT‑T‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCCAGAAAAGACGGCCGATTTCGTTTGTCGCAAACTTGCGGCTCTTGCaaaa > 3:18788/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTACCGGCTCGAGCAAAAc > 8:83991/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTAGCAAACTAGCGGCTCTAGCaaaa > 8:242659/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGACAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCGCTAGCAAAACt > 7:134659/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACt > 1:76065/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATCGCAAACTAGCGGCTCTAGCAAAACt > 7:173887/1‑138 (MQ=255)
aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTTGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGGCGCACCCCGCAAGAAAAGACGGCCGATTTATTTTGTAGCAACCAAGCGGCTGGAACAAAAcaaa > 6:3270/1‑136 (MQ=255)
aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGCTTTGTTTTCTCGCAAACGATCGGAGCTAGCaaaagtga > 6:103842/1‑135 (MQ=255)
ccAAAGGTTTCATACAAAAACACCCCACCGCTTCTTTTTGCCCGCCCCC‑T‑T‑TTT‑ACCCCGCCCGTTTACTCCGCCCCCCCCCCCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 3:230315/138‑1 (MQ=255)
caaaccGTTCCATACAAAAACAGCCCACCGCTTCTTTTGGGCAGCCCCCTT‑T‑TTT‑A‑CCCCCCGGTTTCCTCCCCCGCACCCCCAAACAAACCACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCAt < 6:262056/134‑1 (MQ=255)
aaaCTTTTAATATAAAAAAATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCCGCCCTTTTTCTCAGCCGCAGCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa < 7:246969/139‑1 (MQ=255)
aaaCGTTTCATAAAAAAACATCCCTCCGCTTTTTTTTGGCTGGCAGC‑CTT‑TTT‑A‑GCCGCCGTTTTTGTCCGCCGCAGCCCGCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa < 3:145451/139‑1 (MQ=255)
ccGTTACAAACAAAAACACCCCTCCGCTTCTTTTTGCCCGCCCCC‑C‑T‑TTTAA‑CCCGCCCGTTTTCCCCCCCCCCCCCCCAAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 2:10077/138‑1 (MQ=255)
acttttAATACAAAAACATCCCACCGCTTCTTTTTGGCTCGCAGCGT‑T‑TTT‑A‑ACAGCCGGTTTTCTCAGCCCCCGCCCGCAAGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 7:192021/136‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATGTCTTTTCTCGCAAACGTCCGGCTCAAGCAAAACTCCTGAct > 3:56788/1‑139 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CAT‑TTT‑A‑GCAGCCCGTTTTCTAAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTATTCTCGCAAACTAGCGGCTAAAGAAAAACACATGCct > 4:253740/1‑139 (MQ=255)
ttCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATATTCTCGCAAACTAGCGGCTCTAGCAAAACTCAAGACTCAAt > 7:200463/1‑139 (MQ=255)
cccTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCATTTATCGCAAACAAGCCGCTCGAGCAAAACTCATTCATCTATTATAGACCGTggga > 5:189382/1‑136 (MQ=255)
|
TGAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑T‑TTT‑A‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAA > CP006881/3725068‑3725315
|
| 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
