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 |
|
A16 F57 I0 R4
|
226 |
68.5 |
3221688 |
95.0% |
3060603 |
125.7 |
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 | 88.0%
| 60.8
/ 3.5
| 25 | intergenic (‑37/‑492) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base T (14/6); total (16/9) |
| Fisher's exact test for biased strand distribution p-value = 2.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| 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. |
AATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATA > CP006881/3725075‑3725336
|
aaTAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑‑t‑ttttag > 3:279595/1‑135 (MQ=255)
accgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAACACATCCCTCCGCTTCTTTTTGGCAGGCACC‑CT‑T‑TTTA‑GCAGccc > 7:119860/4‑139 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCGC‑CG‑T‑TTTA‑GCAGGCCGgttt > 6:398195/1‑139 (MQ=255)
ccGCAGTTTTTCTGTCCGGCGTCACCCAGTTCCTCAAAAAGACCATCCACACCCGGAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCGGGCAGC‑C‑‑TATTTT‑GCAGCCCGTTTtctcca > 3:85857/1‑137 (MQ=255)
cTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGGAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGcccg < 5:70457/138‑2 (MQ=255)
tCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGcccgc > 4:159706/1‑134 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGcccg < 1:87726/120‑2 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGcccg > 2:87726/1‑119 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtt > 7:180560/1‑139 (MQ=255)
cccGAAAAGAAACCACCACACGTTAAATCCAAACACATCCCTCCCCTGCTTTGTGGCCGCCAGCTT‑‑T‑TTTA‑GCAGCCCGTTTTCGCAGCCCCAGCCCGCACCAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGc < 2:317527/139‑1 (MQ=255)
agcctAAACATACAAGAAAATGTTAAAAACAAAAACATCCCCCCGCTTCTTTTTGGCTGGCAGC‑CT‑T‑TTTC‑GCCGCCGTTTTGCTCAGCCGCCGCCCGCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGc < 1:366089/135‑1 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTATCAGCCGCAGCCCCCAAGAAAAGACCGCCGATTTATTTTATCGCAAACTAGCGGcactt > 5:136696/1‑138 (MQ=255)
ctaTACAAGCAAAGCTTCAATATAACAACACCCCACGGCTTTTTTTTGCCAGCCCGC‑C‑‑T‑TTTACGCACCCCTTTTTCCCCGCCCCCCCCCCCACCACACGCCGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 4:85857/137‑1 (MQ=255)
aGACACAACCAAACGTTTCATACAAAAACACCCCCCCGCTGCTTTTTGGCAGCCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTCCCCCGCCCCCCCCCGCAAGAACAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:389399/139‑1 (MQ=255)
aCAAGCAAACGTTTCATAGAAACACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTGTCTCGCCAACTAGCGGCGCGAGCAAAAc > 4:157821/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACGAGCGGCTCTAGCAAAAc > 7:388881/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTCCTTTTCTCGCAAACTAGCGGCTCTAGAAAAAc > 3:126720/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACAACCGGCTCTAGCaaaa > 5:279602/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTAAGCCGCCGCCCGCAAAAAAAGACGGCCGATTTAGTTTCTCGCAAACTACCCGCACAAGCaaaa > 5:128703/1‑138 (MQ=255)
aaGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCATTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCACCCCGCAAGAAAACACGGCCGATTTATATTCACGCAAACAAGCGGCGCTAGCAAAAccg > 2:366089/1‑137 (MQ=255)
aaaaCTTTTCATCTAAAAACATCCCGCGGGTTC‑TTTTGGCACGCAGC‑CCTT‑TTTC‑GCGGCCGGTTTTCTCACCCGCTCCCCGAAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATg < 7:75327/138‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTtct < 6:80759/66‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTA‑GCAGCCCGTTTtct > 5:80759/1‑66 (MQ=255)
cccTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTa‑gcag > 6:122851/1‑37 (MQ=255)
cccTCCGCTTCTTTTTGGCAGGCAGC‑CT‑T‑TTTa‑gcag < 5:122851/37‑1 (MQ=255)
ggcagC‑CT‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATCGCAAACTAGCGGCGCGAGCAAAACTCATGCCGGGATGAAAGCCCGTGGAAAGAGAATTGATTTTCACAata > 2:402160/1‑139 (MQ=255)
|
AATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑‑T‑TTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATA > CP006881/3725075‑3725336
|
| 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
