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 F56 I0 R1
|
198 |
55.3 |
2323794 |
95.3% |
2214575 |
126.9 |
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 | 85.4%
| 109.7
/ 11.4
| 41 | intergenic (‑37/‑492) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base . (1/5); new base T (21/11); total (25/16) |
| Fisher's exact test for biased strand distribution p-value = 6.47e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.45e-01 |
| 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. |
GAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑T‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAA > CP006881/3725069‑3725321
|
gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑t‑t > 3:119013/1‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGt > 7:21807/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGt > 7:169870/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CGT‑TTTAGCAGCCCgg > 1:254570/2‑138 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCCCACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CGT‑TTTAGCAGCCCGgtt > 1:71154/1‑138 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCGC‑CTT‑TTTAGCAGCCCGttt > 5:200318/1‑138 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGtttt > 4:179971/1‑139 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CGT‑TTTAGCAGCCCGttt > 5:196234/1‑138 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGAGACAAGCACACGTTTCATAGATAAACATCCAGCCGCGTCGGTTTGGCAGGCAGC‑C‑TGTTTTGCAGCCCGtttg > 8:213519/1‑138 (MQ=255)
cAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTtct < 3:179971/139‑1 (MQ=255)
cTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGcccg < 7:236836/138‑2 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCGGAtt > 8:78097/1‑139 (MQ=255)
catcaAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttc > 4:81683/1‑139 (MQ=255)
aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCaaa > 8:187875/1‑138 (MQ=255)
tCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCCAAc > 4:240591/1‑138 (MQ=255)
acCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTtct > 1:225813/1‑86 (MQ=255)
acCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTtct < 2:225813/86‑1 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAAGATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCGGCCCGTTTTCTCAGCCGCAGCCCGCAACAAACGAAGGCCGATTTCTTTTATCGCAAACTACCGGctc > 7:140166/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTGGCAGCCCGGTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGctc > 8:118372/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc > 7:173841/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCATTTATCGCAAACTAGCGGctg > 3:31481/1‑136 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCCAGAAAAGACGGCCGAGTTCTTTTAGCGCCAACAATCGGcgcaa > 4:14852/1‑135 (MQ=255)
aaGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAg > 3:108276/1‑138 (MQ=255)
ctaTACAACCAACCTTTTAATACAAAAACAACCCTCCGCTTCTTTTTGGCAGGCAGCTT‑T‑TTTCGCAGCCCTTTTCCTCCGCCGCAGCCCCAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 8:173841/137‑1 (MQ=255)
aGATACACGAAAACGTTTCATAGAAAAACACCCCTCCGCTTCTTTTTCGCCGCCAGCGT‑T‑TTTCGCAGCCCGTTTTCTCAGCCGCACCCCGCAACAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:118372/139‑1 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa > 6:107549/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa > 7:19065/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc > 5:24653/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc > 5:289979/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTATCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTACTTTTCTCGCAAACTACCGGCTCTAGCaaaa > 8:187100/1‑138 (MQ=255)
gaaacggTTTCATCTAAAAACATCCCTCCGATTCTTTTTGGCTGGCAGCTT‑T‑TTTCGCAGCGCGTTTTCTCAGCCGCAGCCCGAAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 7:187100/133‑1 (MQ=255)
gCAAACGTTTCATATAAAACCACCCCTCCGCTTCTTTTTGCCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCCGCCCCAGCCCGCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 3:81683/139‑1 (MQ=255)
ccAAACTTTTCATAAAAAAACATCCCACCGCTTCTTTTTGCCAGGAAGC‑CTT‑TTTCTCACCCGGTTTTCTCCGCCGCCGCCCCCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 3:240591/138‑1 (MQ=255)
aaCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAc < 7:187875/139‑1 (MQ=255)
acttttCATAAAAAAACATCCCTCCGCTTCTTTTTGGCCGGCAGCTT‑T‑TTTAGCCGCCCGTTTTCTCAGCCGCCGCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 4:108276/136‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 5:107549/139‑1 (MQ=255)
aCGTTTAATATAAAAAAATCCATCGGCTTATTTTTGGATGGCAGCGT‑T‑TTTTGATCCCCTTTTTCTCAGCCCCAGCCCGAATTAAAAGACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCATGAct < 8:19065/139‑1 (MQ=255)
aCGTTACAAACAAAAACATCCCACCGCTTCTTTTTGGCAGGCACC‑CTT‑TTTAGCCCCCGGTTTGCTCAGCCCCCGCCCCCAACAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 7:177750/139‑1 (MQ=255)
aaaaaCATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAc < 6:289979/139‑1 (MQ=255)
cTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:72249/106‑1 (MQ=255)
cTCCGCTTCTTTTTGGCAGGCAGC‑CTT‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa > 8:72249/1‑106 (MQ=255)
cGCTTCTTTTTGGCCGGCCGC‑CTT‑TTTCGCAGCCCGTTTCCTCAGCCGCAGCCCCCAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGaa < 6:120890/139‑1 (MQ=255)
|
GAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑T‑TTTAGCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAA > CP006881/3725069‑3725321
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
