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 |
|
A67 F1 I1 R1
|
17 |
65.0 |
4212288 |
95.3% |
4014310 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,175,232 |
(T)6→7 |
coding (877/933 nt) |
pbpG ← |
D‑alanyl‑D‑alanine endopeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,175,226 | 1 | . | T | 97.1%
| 130.5
/ ‑3.4
| 35 | coding (883/933 nt) | pbpG | D‑alanyl‑D‑alanine endopeptidase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (13/21); total (14/21) |
| Fisher's exact test for biased strand distribution p-value = 4.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGAGTATCGCCATCCGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑G‑TTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCAGGCG > REL606/2175152‑2175295
|
cAGAGTATCGCCATCCGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCCTTT‑TGGCGG‑G‑TTTTT‑G‑t > 2:980414/1‑76 (MQ=255)
cAGAGTATCGCCATCCGAATTCACTTAATCGTTCTGTGCCGTCGGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑G‑t < 1:558840/76‑1 (MQ=255)
gTATCGCCATCCGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑G‑ttttt < 2:1728889/76‑1 (MQ=255)
aTCGCCATCCGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑G‑ttttttt < 2:206701/76‑2 (MQ=255)
gCCATCCGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCGCCCCCCCTTT‑GGGGGG‑G‑ttttt‑t‑ttttttttt > 1:1646963/1‑73 (MQ=255)
cATCCGATTTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGc < 1:1434882/76‑1 (MQ=255)
ccGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCa < 2:520747/76‑1 (MQ=255)
ccGAATTCACTTAATCGTTCTGTGCCGCCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCa < 1:782233/76‑1 (MQ=255)
aatttCCCTTATCCGTGCTGTGCCGTCGGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAAc < 1:575651/73‑1 (MQ=255)
aaTTCACTTAGTCGTTCTGTGCCTTCGCCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACg < 2:1685760/76‑1 (MQ=255)
tCACTTAATCTTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACgctg < 2:629987/76‑1 (MQ=255)
tCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCCTTT‑GGGGGG‑CTTTTTT‑T‑TTTTTTTTTGCTCAACgctg > 1:1894933/1‑76 (MQ=255)
cTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGctgctg < 2:2055809/76‑1 (MQ=255)
aaTCTTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCg < 1:733655/76‑1 (MQ=255)
tgtgCCGTCTGCCCCGCCGCCCCCCCTTT‑GGGGGC‑T‑TTTTT‑T‑TTTTTTTTTGCTCAACGCTGCTGCCGGCCCAGGc > 2:1611257/1‑76 (MQ=255)
tgtgCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGc > 2:385965/1‑76 (MQ=255)
gggCCGTCGGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCa < 2:1609173/74‑1 (MQ=255)
ccGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGGATCa > 2:1805663/1‑76 (MQ=255)
ccGTCTGCCCCGCCG‑CCCCCCTTTGGGGGGG‑T‑TTTTT‑T‑TTTTTTTTAGCTCAACGCTGCTGCCGGCACAGGCATCa > 2:1871884/1‑76 (MQ=255)
ccGTCTGCCCCGCCG‑CCCCCCCTT‑TGGCGGCC‑TTTTT‑T‑TTTTTTTTTTTTCAACCCTTCTGCCCGCCCACGCCTCa > 2:317158/1‑76 (MQ=255)
ccGTCTGCCCCGCCC‑CCCCCATTT‑TGGCGG‑G‑TTTTTGG‑TTTTTTTTAGCTCAAAGCTGCTGCCTGCACAGGCATCa > 2:183861/1‑76 (MQ=255)
ccgCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACttt < 1:454349/74‑1 (MQ=255)
tcccccGCCG‑CCGCCATTG‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTa < 1:940951/74‑1 (MQ=255)
ccccGCCG‑CCGCCCTTT‑TGGCGG‑C‑TTTTT‑GTTTTTTTATAATTCTACCAGGCTGCAGGCACAGGGAACACCTTAcc > 2:768045/1‑76 (MQ=255)
cccGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCg > 2:500802/1‑76 (MQ=255)
cccccg‑ccgccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCgg < 1:1322688/73‑1 (MQ=255)
cgccg‑ccgcCATTT‑TGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAATGCTGCAGCCGGCCCAGGCATCACTTTACCGGt > 2:664863/1‑76 (MQ=255)
cgccg‑ccgcCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGt > 2:746078/1‑76 (MQ=255)
cgccg‑ccgcCATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGAATAACTTTACCGGt > 2:32293/1‑76 (MQ=255)
gccg‑ccgccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGtt > 2:1191074/1‑76 (MQ=255)
gccg‑ccgccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGtt > 2:1236041/1‑76 (MQ=255)
ccg‑ccgccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCCCAGGCATCACTTTACCGGttt > 2:1307950/1‑76 (MQ=255)
cg‑ccgccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTc < 2:1289028/76‑1 (MQ=255)
g‑ccgccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCa < 2:274567/76‑1 (MQ=255)
ccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATcc > 2:1379177/1‑76 (MQ=255)
ccATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATcc < 1:2004917/76‑1 (MQ=255)
cATTT‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCa < 2:1093466/76‑1 (MQ=255)
ttt‑GGGCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAgg < 1:1436315/76‑1 (MQ=255)
gggCGG‑C‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTAc > 2:1075354/1‑76 (MQ=255)
ggcgg‑c‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACg < 1:3422/76‑1 (MQ=255)
ggcgg‑c‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACg < 2:461207/76‑1 (MQ=255)
cgg‑c‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCa > 2:654474/1‑76 (MQ=255)
cgg‑c‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCa > 1:1489303/1‑76 (MQ=255)
gg‑c‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCAg < 1:742522/76‑1 (MQ=255)
g‑c‑TTTTT‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCAgg < 1:565863/76‑1 (MQ=255)
ttttt‑GTTTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCAggcg > 2:779480/1‑76 (MQ=255)
|
CAGAGTATCGCCATCCGAATTCACTTAATCGTTCTGTGCCGTCTGCCCCGCCG‑CCGCCATTT‑GGGCGG‑C‑TTTTT‑G‑TTTTTTATAGCTCAACGCTGCTGCCGGCACAGGCATCACTTTACCGGTTTCAATCCAGGTACGCAGGCG > REL606/2175152‑2175295
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
