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 |
|
A19 F53 I0 R3
|
198 |
62.2 |
2365906 |
95.5% |
2259440 |
127.1 |
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 | 90.4%
| 127.0
/ 10.7
| 52 | intergenic (‑37/‑492) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base . (1/4); new base T (28/16); total (32/20) |
| Fisher's exact test for biased strand distribution p-value = 1.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.59e-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. |
TGAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑T‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAA > CP006881/3725068‑3725316
|
tGAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑t > 4:267661/1‑139 (MQ=255)
tGAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTGTTTTTGGCAGGCAG‑c‑cg > 1:152591/1‑138 (MQ=255)
gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCCCCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGATAAACATCCCTCCGCTTCTTTTTGGCAGGCTG‑C‑C‑t‑t > 2:79775/1‑139 (MQ=255)
gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCCG‑C‑C‑t‑t > 2:274813/1‑139 (MQ=255)
gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑t‑t > 3:250682/1‑139 (MQ=255)
gAGCCGAATAGACCGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAG‑C‑C‑t‑t > 4:141423/1‑139 (MQ=255)
accgctgCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCAAACCCGTAAAGATACAAGCAAACGATTCATAGAAAAACATCCCTCCGCTTCATTTTGTCAGGCAG‑C‑CTT‑TTTAGCAGccc > 1:23048/7‑139 (MQ=255)
accgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTTGCAGGCAG‑C‑CTT‑TTTAGCAGccc > 8:36197/4‑139 (MQ=255)
accgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGATCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGccc < 8:110055/136‑1 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGt > 5:280972/2‑139 (MQ=255)
cgCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTGCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGt > 6:200874/2‑139 (MQ=255)
ggCTGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGttt > 6:141936/1‑138 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATTCAAGCAAACGTTTCATTGAACAACATCCCTCCGCTTCTTTTGTGCAGGCAG‑C‑CGT‑TTTAGCAGCCCGttt > 4:145250/1‑138 (MQ=255)
ggCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGtttt > 6:140468/1‑139 (MQ=255)
ccGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCCCACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCGCCGCGTCTGTTTGGCCGGCTG‑C‑CTT‑TTTAGCAGCCCGGTTt‑ctcgg > 4:222854/1‑137 (MQ=255)
cTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGcccg < 1:261278/138‑2 (MQ=255)
tCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGGTTT‑CTCAGCCGCAGcccgc > 7:126348/1‑134 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtt > 6:290660/1‑139 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CGT‑TTTAGCACCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtt > 5:248937/1‑139 (MQ=255)
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGGGTTTTTGGCAGGCCG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTAAGCCGCAGCCCGCCAGAAAACCCGGCCGCtt > 5:38436/1‑139 (MQ=255)
catcaAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttc > 3:108914/1‑139 (MQ=255)
caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CGT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCCCAAGAAAAGACGGCCGAtttcttt > 7:216765/1‑139 (MQ=255)
accaccCACACCCGTAAAGATACCACCAACCTTTTCATACAAAAACACCCCTCCGCTTCTTTTTGGCCGGCAG‑C‑CTT‑TTTCGCCGCCCGTTTT‑CTCCGCCGCACCCCCCAACAAACGACGGCCGATTTCTTTTCTCGCa < 8:126348/139‑1 (MQ=255)
aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGCTTTCTTTTCTCggcaac > 4:49135/1‑134 (MQ=255)
cacaCCCGAAAAGATACACGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCACCCCGTTTT‑CTCAGCCGCAGCCCGCAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAg < 4:87601/139‑1 (MQ=255)
cGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGccc < 4:144147/76‑1 (MQ=255)
cGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGccc > 3:144147/1‑76 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc > 5:209771/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTTTGTCGCAAACTAGCGGcgc > 4:174587/1‑135 (MQ=255)
aGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCAG‑C‑CTT‑TTTAGCCGCCCGTTTG‑CCCAGCCCCAGCCCGCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 3:267661/139‑1 (MQ=255)
gATACAAGCAAAGTTTTAATATAAAAACTTCCCTCCGCTTGTTTTTGCCTGGCAG‑CTT‑T‑TTTAGCAGCCGTTTTT‑CTCCGCCCCAGCCCGCAATAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaa < 8:216765/139‑1 (MQ=255)
aTACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCCGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATATCTTTTCTCGCAAACTAGCGGCTCTAGCaa > 7:59037/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa > 1:153725/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa > 8:209964/1‑135 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTTTCTCGCAAACTAGCGGCTCGAGCaaaa > 2:206170/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCCAACTAGCGGCTCTATCAAAAc > 3:80157/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:209964/135‑1 (MQ=255)
aaGCAAACGTTTAATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGACGCAGCCAGCAAGAAAAGACGGCCGATTTCTTTTCTGGCAAACTAGCGGCTCGAGCaaaaat > 7:239397/1‑136 (MQ=255)
aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAC‑C‑C‑TGTTTAGCAGCCCGTTTT‑CTCACCCCCAGCCCGCAAGAAAAGACGGCCGATATCTATTCTCGCAAACTATCGGCTCAAGCAAAACTCa > 8:98261/1‑139 (MQ=255)
gCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTATAGCAAACAACCGGCTCTAGCAAAACTCAt > 2:24214/1‑139 (MQ=255)
gCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTAAGCCGCAGCCCGCAAGAAAAGACGGCCCAGTTCGTTTATAGCAAACTAGGCGCTGGAGCAAAACGCAt > 1:123458/1‑139 (MQ=255)
ccAAACGTTACATACAAAAACATCCCTCCGCTGATTTTTGGCAGCCAG‑C‑CTT‑TTTAGCAGCCCTTTTT‑CTCAGCCCCAGCCCCCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 5:141936/138‑1 (MQ=255)
aaccGTTCCATATAAAAAAATCCCCCCGCTTTTTTTTGGATGCCAC‑C‑CTT‑TTTAGACGCCCTTTTA‑AACCGCCGCCCCCCGCACTAAAACACGGCCGATTTCTTTTCTCGAAACCTAGCGGCTCTAGCAAAACTCATGa < 8:239397/136‑1 (MQ=255)
aaaCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCCGCCGCCGCCCGCAAGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa < 5:140468/139‑1 (MQ=255)
ccGTTTCATCCAAAAACATCCCGCCGCTTCTTTTTGGCTGGCAG‑C‑CTT‑TTTAGCCCCCCGTTTT‑CTCCGCCGCACCCCCCATTAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 6:280972/138‑1 (MQ=255)
acttttCAAATAAAAAAATCCCTCCGCTTATTTTTGGCCGCCAG‑C‑CTT‑TTTAGCCGCCCGTTTT‑CTCAGCCGCCGCCCGAAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 8:160178/136‑1 (MQ=255)
acttttAATAGAAAAACATCCCTCCGCTGCTTTTTGGCAGGCTG‑C‑CTT‑TTTCCCAGCCGGTTTT‑CACCGCCGCCGCCCGCAAGAACCGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 3:141423/136‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACAGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct > 3:275209/1‑139 (MQ=255)
aCGTTTAATATAAAAACATCCCTCCGATTATTTTTGGCAGGATGAC‑T‑T‑TTTAGCAGCCCTTTTG‑CTCAGCCGCACCCCGCAAAAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 7:98261/139‑1 (MQ=255)
tCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTAt > 7:220237/1‑138 (MQ=255)
tCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCCGCTCTAGCAAAACTCAAGACTCTAt > 1:23684/1‑138 (MQ=255)
cATAGAAAACCAACCCTCCGCTTCTTTTTGCCAGCCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCCCAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGa < 2:9319/139‑1 (MQ=255)
aaaaaCATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCCGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACAAGCGGCTCTAGCAAAACTCAGTACTCgatgatgtgt > 7:251909/1‑135 (MQ=255)
aaaaaCACCCCTCCTCTTCTTTTGGGCCGGCCC‑C‑A‑T‑TTTAACCCCCCCTTTTCCTCCCCCCCCCCCCCCAAAAAACCCCGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAc < 4:108914/139‑1 (MQ=255)
cccTCCGCTTTTTTTTGGCCGGCCG‑CTT‑T‑TTTCGCAGCCGTTTTT‑CACCCCCGCCCCCCCAAACAACACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGaaa < 2:23684/139‑1 (MQ=255)
cccTCCGCTTCTTTTTGGCTGGCAG‑C‑CTT‑TTTAGCAGCCGGTTTT‑CTCCGCCGCAGCCCGAAAGAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGaaa < 8:220237/139‑1 (MQ=255)
gcag‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt > 8:290324/1‑95 (MQ=255)
gcag‑C‑CTT‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCGAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 7:290324/95‑1 (MQ=255)
|
TGAGCCGAATAGACAGCGGCAGCCGCAGTTTTTCTGTCCGGCGTCACCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑T‑TTTAGCAGCCCGTTTT‑CTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAA > CP006881/3725068‑3725316
|
| 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
