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 |
|
A22 F68 I1 R1
|
31 |
72.2 |
3191514 |
95.4% |
3044704 |
126.4 |
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 | 93.8%
| 106.1
/ ‑0.3
| 32 | intergenic (‑109/+45) | pstS/pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (24/6); total (24/8) |
| Fisher's exact test for biased strand distribution p-value = 5.65e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CATAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCG‑TTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCTGCTTC > BS168_reference_genome/2581591‑2581855
|
cATAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCG‑ttt > 2:31698/1‑139 (MQ=255)
tAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCTAATGTTAAGGTTTTGTAAATCAGTGCG‑ttttt > 7:40930/1‑139 (MQ=255)
gCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCG‑tttttttg < 1:43337/139‑3 (MQ=255)
aTTTGTTTTTTTTAATTTCCTGAATTCCCCCTGCGTA‑AAAGTGTTAATTTGCCCAACACGTATACAGAAAAGGTTCTATGTAAAAAGGGTTTTAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATaaa < 2:178009/139‑1 (MQ=255)
ttttttttCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCG‑ttttt > 5:8651/1‑125 (MQ=255)
ttttttttCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCG‑ttttt < 6:8651/125‑1 (MQ=255)
g‑tAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACTCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCag > 7:271294/1‑138 (MQ=255)
g‑tAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCag > 5:66450/1‑138 (MQ=255)
gTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCACAAGAAGtt > 1:190930/1‑139 (MQ=255)
ataGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTg > 4:140079/1‑138 (MQ=255)
gTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCAGCAttt > 5:297916/1‑138 (MQ=255)
tAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttc > 3:155111/1‑139 (MQ=255)
aaGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTATTTATCAGAATACGTTGTGTTTTCTTCATTttct > 7:42870/1‑138 (MQ=255)
aaGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttctt > 7:200668/1‑139 (MQ=255)
aaGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTttct > 7:48691/1‑138 (MQ=255)
aGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGTTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TGTTTTTTTAGTTATAAGAAGACGTTGTGGTTTATGCATTttctt > 2:92392/1‑138 (MQ=255)
aGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGt < 7:58886/105‑1 (MQ=255)
aGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGt > 8:58886/1‑105 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 8:86895/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 5:394271/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 3:196633/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAAttt > 3:183981/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTAAAttt > 3:354747/1‑139 (MQ=255)
cTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGAAGTTGTGTTTTCTGCATTTTCTTCAAttt > 8:362452/1‑139 (MQ=255)
aTGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTg > 3:162957/1‑139 (MQ=255)
agaccgggTTTCAACCTAATTTTAAGTTTTTTTAAATCAGTGCGTTTTTTTTT‑AAAAAAAAAACGCCCACATCATGTGAGCG‑TTCTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCtt < 8:394416/134‑1 (MQ=255)
gaaaGGGTTTGAACCGATTGTTATGGTTTTTTAAATCAGTGGGTTTTTTTTT‑AAAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCtt < 2:60774/137‑1 (MQ=255)
aaaGGGTTTCAACCGAATGTAACCGTGTTGTAAATCAGTGCG‑TTTTTTTTAATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTa < 4:354747/139‑1 (MQ=255)
ttGAACCGAATGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCtttt > 5:166402/1‑139 (MQ=255)
ctaaTTTTATGTTTTTTAAAATCTGTGCT‑TTTTTTTTAAAAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAg < 6:394271/137‑1 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGcctgtc > 1:60774/1‑133 (MQ=255)
aaTGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTGTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGcctgtct > 7:394416/1‑133 (MQ=255)
aTGTTAAGGTTTTGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAACACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTAc < 3:140079/139‑1 (MQ=255)
ttGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTTAGTTATCagaag > 8:290289/1‑75 (MQ=255)
ttGTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCGTTTTTTTTTTAGTTATCagaag < 7:290289/75‑1 (MQ=255)
gTAAATCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCTg > 1:177573/1‑139 (MQ=255)
aTCAGTGCGTTTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCTGCTTc > 7:87098/1‑139 (MQ=255)
|
CATAAGCACCAATTTGTTTTTTTTCATTTCCTGAATTCCCCCTGCGTATAATGTG‑TAATTTGTCCTACACGTATAGAGTAAAGGTTCTATGTAAAAAGGGTTTGAACCGAATGTTAAGGTTTTGTAAATCAGTGCG‑TTTTTTGT‑ATAAAAAAAACGCCCACATCATGTGAGCG‑TTTTTTTTTAGTTATCAGAAGACGTTGTGTTTTCTGCATTTTCTTCAATTTTGTCTTTATTCTTTTGCTGAGTACCTTCTTTGTCCTGCTTC > BS168_reference_genome/2581591‑2581855
|
| 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
