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 |
|
A1 F2 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,759,822 |
A→G |
F23S (TTC→TCC) |
menI ← |
1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,759,822 | 0 | A | G | 96.9%
| 110.0
/ NA
| 32 | F23S (TTC→TCC) | menI | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (12/19); minor base C (0/1); total (12/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AACCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGAACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTA > NZ_CP009273/1759735‑1759905
|
aaCCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGAc > 1:205360/1‑90 (MQ=255)
aaCCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGAc < 2:205360/90‑1 (MQ=255)
ctgctTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑tt < 2:130372/90‑1 (MQ=255)
ctactTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑tt < 1:743444/87‑1 (MQ=255)
gctTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGAc < 2:98659/77‑1 (MQ=255)
gctTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGAc > 1:98659/1‑77 (MQ=255)
gctTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTc < 2:619551/90‑1 (MQ=255)
tGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTc < 1:416032/90‑1 (MQ=255)
gTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCa < 2:676428/90‑1 (MQ=255)
cgAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCAt < 1:1052576/90‑1 (MQ=255)
cgAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCAt > 1:837782/1‑90 (MQ=255)
gAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATa < 1:87105/90‑1 (MQ=255)
tGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTc > 2:966065/1‑90 (MQ=255)
tgtCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTcc < 1:701473/90‑1 (MQ=255)
gtCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATGTTTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTcc > 1:620271/1‑90 (MQ=255)
ccAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCat > 1:20906/1‑90 (MQ=255)
ccAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCat < 1:6663/90‑1 (MQ=255)
ccAATATGTTCAAAGCGAATATCCAGGCCCCCCCCCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCat < 1:232497/90‑1 (MQ=255)
atatGTTCAAAGCGAATATCCAGGGACCCCACCATGTTTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCatat < 2:620271/90‑1 (MQ=255)
atatGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATc > 2:95051/1‑90 (MQ=255)
ttCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTta > 2:634520/1‑90 (MQ=255)
cAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTtaat > 1:306963/1‑90 (MQ=255)
aaGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCa < 2:413638/40‑1 (MQ=255)
aaGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCa > 1:413638/1‑40 (MQ=255)
aaGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTtaataa < 2:901797/90‑1 (MQ=255)
gCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAAtc < 2:20906/90‑1 (MQ=255)
gCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAAtc < 1:634520/90‑1 (MQ=255)
aaTATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGt < 2:504184/46‑1 (MQ=255)
aaTATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGt > 1:504184/1‑46 (MQ=255)
aaTATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTcc > 2:340419/1‑90 (MQ=255)
tCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTa < 1:704213/90‑1 (MQ=255)
tCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTa < 1:1025224/90‑1 (MQ=255)
|
AACCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGAACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTA > NZ_CP009273/1759735‑1759905
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTCCATGCAGCAACCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGAACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTAAAGCCTGCACA > NZ_CP009273/1759723‑1759916
|
CCTCCATGCAGCAACCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGG < SRR3722213.760240/100‑1 (MQ=60)
gcatacgagataataacgggtctcgtgggctcggagatgtgtataagagacaGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGAC < SRR3722213.753271/48‑1 (MQ=60)
TCCATGCAGCAACCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGAC > SRR3722213.209877/1‑100 (MQ=60)
CCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑Tctg > SRR3722213.100906/1‑97 (MQ=60)
CTACTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCC < SRR3722213.760181/100‑1 (MQ=60)
GCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCAT > SRR3722213.856405/1‑100 (MQ=60)
TGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCA < SRR3722213.425378/100‑1 (MQ=60)
CGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGT < SRR3722213.1075773/100‑1 (MQ=60)
GAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTG < SRR3722213.89086/100‑1 (MQ=60)
CTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATGTTTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCC > SRR3722213.634208/1‑100 (MQ=60)
GGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCAT > SRR3722213.21407/1‑100 (MQ=60)
TGTCATCACCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATAT < SRR3722213.717238/100‑1 (MQ=60)
CCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAAT > SRR3722213.313637/1‑100 (MQ=60)
CCAATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAAT < SRR3722213.6809/100‑1 (MQ=60)
CCAATATGTTCAAAGCGAATATCCAGGCCCCCCCCCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAAT < SRR3722213.237533/100‑1 (MQ=60)
AATATGTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGctgtctcttatacacatctccgagcccacgagacccgtta > SRR3722213.422915/1‑60 (MQ=60)
GTTCAAAGCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGctgtctcttatacacatctccgagcccacgagac > SRR3722213.515559/1‑66 (MQ=60)
GCGAATATCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTAAAG < SRR3722213.648775/100‑1 (MQ=60)
TCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATctgtctcttatacacatctcc > SRR3722213.232521/1‑79 (MQ=60)
TCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTAAAGCCTGCAC < SRR3722213.720043/100‑1 (MQ=60)
TCCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTAAAGCCTGCAC < SRR3722213.1047745/100‑1 (MQ=60)
CCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTctgtctcttatacacatctccgagcccacgagacccgttattatctcgtatgccgtctt > SRR3722213.418893/1‑41 (MQ=60)
CCAGGGACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTAAAGCCTGCACA > SRR3722213.846482/1‑100 (MQ=60)
|
CCTCCATGCAGCAACCCGAAAGGCTGCTTTGTCCGCGAGTCTACTGGCATTGTCGCTTCAAGGGTGTCATCACCAATATGTTCAAAGCGAATATCCAGGAACCCCACCATG‑TTTCCTTCACCCATAGCATTCAGTGCTTCCAGGGTGATTTTCCGTTTCCATATCATTTAATAATCTCCAGTAAAGCCTGCACA > NZ_CP009273/1759723‑1759916
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
