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 |
|
A23 F66 I1 R1
|
33 |
61.7 |
2789148 |
95.4% |
2660847 |
127.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
BS168_reference_genome |
2,581,732 |
(T)6→7 |
intergenic (‑115/+39) |
pstS ← / ← pbpA |
phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | BS168_reference_genome | 2,581,726 | 1 | . | T | 88.9%
| 171.6
/ 13.8
| 54 | intergenic (‑109/+45) | pstS/pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| Reads supporting (aligned to +/- strand): ref base . (1/5); new base T (42/6); total (43/11) |
| Fisher's exact test for biased strand distribution p-value = 7.87e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑G‑TTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCTGCTTCGA > BS168_reference_genome/2581593‑2581857
|
tAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑G‑ttttt > 3:224990/1‑139 (MQ=255)
tAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑G‑ttttt > 4:278092/1‑139 (MQ=255)
aTTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTATTGTAAATCAGT‑G‑CTT‑TTTTTTGT‑ATaa > 3:202538/1‑138 (MQ=255)
tttttCATTTCGTGAATTCCCCCTCCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTCCTATGAAAAAAGGGTTTCAACCTAATGTAACGGTTTTTTAAATCAGG‑G‑C‑GTTTTTTTGA‑ATAAAAAAAACg < 8:200919/138‑1 (MQ=255)
tttttCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATaaaaaaaaacg > 7:14947/1‑136 (MQ=255)
tttCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGcc > 7:310446/1‑138 (MQ=255)
ccccTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑ttt > 3:138318/1‑139 (MQ=255)
gtAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTTAGTTaa > 6:20345/1‑135 (MQ=255)
tAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCag > 3:268657/1‑137 (MQ=255)
tCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTtg > 4:106843/1‑139 (MQ=255)
ccTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTtgt > 3:316953/1‑139 (MQ=255)
caaccacTTATACTGTAACGTTTATATTAAAAACGGGTTTCAACCTAATTTTAAGGTTTTGAAAATCTGG‑G‑G‑G‑TTTTTTTTAAAAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTtgt < 7:304867/135‑1 (MQ=255)
ataGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTTGTTATCAGAAGACGTTGTGTTTTCTg > 1:317643/1‑138 (MQ=255)
ataGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTg > 7:86194/1‑138 (MQ=255)
ataGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTg > 4:293560/1‑138 (MQ=255)
tAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCTTTttc > 6:58449/1‑139 (MQ=255)
tAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttc > 6:93238/1‑139 (MQ=255)
tAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttc > 1:253020/1‑139 (MQ=255)
aatcttCTATGTAAAAAGGGTTTGAACCGAATGTTAATTTATTATAAATCAGT‑G‑A‑GTTTTTTTGT‑ATAAAAAAAACGCCAACATCATGTGAGCG‑ATTTTTTTTATTTATCATAAGAATTTGTGTTTTCTGCATTttct > 4:317546/5‑138 (MQ=255)
aaGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 3:64557/1‑139 (MQ=255)
aaGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 8:90772/1‑139 (MQ=255)
aaGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 1:11927/1‑139 (MQ=255)
aGGTTCTATGTAAAAAGGGTTTGATCCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttcgt > 4:12656/1‑136 (MQ=255)
aGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 3:115176/1‑138 (MQ=255)
gTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCaa > 5:150924/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCTGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATGAGAAGACGTTGTGTTTTCTGCATTATCTTCAAttt > 3:126673/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCATAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 5:30092/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 6:33873/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 6:36304/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 1:238629/1‑139 (MQ=255)
tATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGA‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt < 7:90772/138‑1 (MQ=255)
tttAAAATGGGTTTGACCCTAATGTTAAGGTTTTTTAAATCAGG‑G‑C‑GTTTTTTTTT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt < 3:278092/134‑1 (MQ=255)
aaaaGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCttt > 1:305163/1‑139 (MQ=255)
aaaGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTATTTATCAGAAGACGTTGTTTTTTATTCATTTTATTCAATTTTTTCattt > 6:217615/1‑138 (MQ=255)
aaaGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTa > 8:80146/1‑139 (MQ=255)
gTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGCCGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTTTTCtt > 6:68666/1‑139 (MQ=255)
gTTTCAACCGATTTTTATGGTTTTTAAAATCAGT‑G‑CTT‑TTTTTTTT‑AAAAAAAACACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCtt < 2:253020/139‑1 (MQ=255)
ttGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCtttt > 5:64956/1‑139 (MQ=255)
ttGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTAtttt > 7:308970/1‑139 (MQ=255)
ttGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTATTTATTCtttt > 3:228234/1‑139 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTa > 1:320450/1‑139 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTa > 5:335553/1‑139 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTa > 2:250986/1‑139 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTa > 1:30559/1‑139 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTa > 2:296814/1‑139 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCAACATCATGTGAGCG‑TTTTTTTTTATTTATAAGAAGACGTTGTGTTTTAATCATTTTATTAAATTTTGTATTTATTCTTTTTCttatta > 4:41501/1‑134 (MQ=255)
aaTGTTAAGGTTTTGTAAATAAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTATTTATCAGAAGACGTTGTGTTTACTCAATTATCTTCAATTTTGTATTTATTCTTTTGCTGAGTa > 8:29936/1‑139 (MQ=255)
ttGTTATGTTTTTTTAAATCAGT‑GTT‑T‑TTTTTTTT‑AAAAATAACACGCCCTCATCATGTGAGCG‑GTTTTTTTTAGTTATCAGAAGACGTGGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 4:126673/138‑1 (MQ=255)
atgttatgttTTTTTAAATCAGTGG‑T‑T‑TTTTTTTT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 8:308970/139‑1 (MQ=255)
aTGTTACGGTTTTGTAAATCAGT‑G‑CTT‑TTTTTTTT‑AAAAAAAACACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 4:64557/139‑1 (MQ=255)
aTGTTAATGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 7:118781/139‑1 (MQ=255)
aTGTTAAGGTTTTGTAAATCAGT‑G‑C‑GTTTTTTTGT‑AAAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGt < 3:106843/137‑1 (MQ=255)
tGTTATGTTTTTGTAAATCAGT‑G‑G‑GTTTTTTTTT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 4:316953/138‑1 (MQ=255)
tGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCt > 7:274519/1‑139 (MQ=255)
tGTAAATCAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCt > 4:308317/1‑139 (MQ=255)
cAGT‑G‑C‑GTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTATTTATCAGAAGACGTTTTGTTTTCTGCATTTTGTTAAATTTTGTATTTATTGTTTTTATGAGTTCCTTCTTTGTCATGCTTCGa > 2:340616/1‑139 (MQ=255)
|
TAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTGTAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGT‑G‑C‑G‑TTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCTGCTTCGA > BS168_reference_genome/2581593‑2581857
|
| 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
