mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NC_001416‑0 | 138 | Δ1 bp | 100% | intergenic (–/‑53) | – / → nu1 | –/DNA packaging protein |
| RA | NC_001416‑1 | 4,566:1 | +G | 100% | intergenic (+139/‑10) | L → / → K | tail component/tail component |
| RA | NC_001416‑2 | 1,261 | A→G | 100% | K338E (AAA→GAA) noncoding (107/621 nt) |
orf‑401 → orf206b ← |
Tail fiber protein |
| RA | NC_001416‑2 | 1,432:1 | +C | 100% | coding (1183/1206 nt) | orf‑401 → | Tail fiber protein |
| RA | NC_001416‑2 | 2,314 | G→A | 100% | S229N (AGC→AAC) | orf‑314 → | Tail fiber |
| MC JC | NC_001416‑2 | 2,338 | Δ5,996 bp | 100% | [orf‑314]–ea59 | [orf‑314], orf‑194, ea47, ea31, ea59 | |
| RA | NC_001416‑3 | 1,915 | T→C | 100% | pseudogene (9/186 nt) noncoding (181/192 nt) |
orf61 ← orf63 ← |
hypothetical protein hypothetical protein |
| RA | NC_001416‑3 | 5,327 | T→G | 11.2% | intergenic (‑71/‑54) | orf28 ← / → lambdap48 | hypothetical protein/Superinfection exclusion protein B |
| RA | NC_001416‑3 | 5,833 | A→G | 100% | G151G (GGA→GGG) | lambdap48 → | Superinfection exclusion protein B |
| RA | NC_001416‑3 | 8,714 | Δ1 bp | 100% | coding (126/714 nt) | cI ← | repressor |
| RA | NC_001416‑4 | 6,817 | T→C | 100% | F42F (TTT→TTC) | R → | endolysin |
| RA | NC_001416‑4 | 7,335 | T→C | 7.9% | R57R (CGT→CGC) | Rz → | cell lysis protein |
| RA | NC_001416‑4 | 7,353 | G→A | 8.4% | A63A (GCG→GCA) | Rz → | cell lysis protein |
| RA | NC_001416‑4 | 7,356 | C→G | 6.6% | L64L (CTC→CTG) | Rz → | cell lysis protein |
| RA | NC_001416‑4 | 7,361 | C→A | 5.5% | A66E (GCA→GAA) | Rz → | cell lysis protein |
| RA | NC_001416‑4 | 7,384 | G→A | 8.8% | D74N (GAT→AAT) | Rz → | cell lysis protein |
| RA | NC_001416‑4 | 7,389 | T→G | 11.0% | A75A (GCT→GCG) L2R (CTA→CGA) |
Rz → Rz1 → |
cell lysis protein Rz1 protein |
| RA | NC_001416‑4 | 7,629 | T→C | 23.9% | intergenic (+3/+29) | Rz → / ← bor | cell lysis protein/Bor protein precursor |
| RA | NC_001416‑4 | 7,796 | G→A | 26.3% | V52V (GTC→GTT) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,807 | T→C | 21.0% | K49E (AAG→GAG) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,811 | C→T | 20.9% | G47G (GGG→GGA) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,820 | A→C | 17.3% | S44S (TCT→TCG) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,832 | A→G | 14.5% | H40H (CAT→CAC) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,858 | C→T | 13.8% | A32T (GCA→ACA) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,867 | C→T | 11.1% | A29T (GCA→ACA) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,878 | T→C | 10.9% | Q25R (CAA→CGA) ‡ | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,879 | G→C | 11.5% | Q25E (CAA→GAA) ‡ | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,918 | G→T | 6.8% | L12M (CTG→ATG) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 7,919 | G→T | 6.6% | A11A (GCC→GCA) | bor ← | Bor protein precursor |
| RA | NC_001416‑4 | 8,134 | G→T | 7.0% | intergenic (‑183/+107) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,141 | C→G | 14.4% | intergenic (‑190/+100) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,151:1 | +C | 15.0% | intergenic (‑200/+90) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,152 | T→A | 16.4% | intergenic (‑201/+89) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,152:1 | +A | 100% | intergenic (‑201/+89) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,184 | C→T | 100% | intergenic (‑233/+57) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,191 | C→T | 100% | intergenic (‑240/+50) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,203 | G→A | 100% | intergenic (‑252/+38) | bor ← / ← lambdap78 | Bor protein precursor/putative envelope protein |
| RA | NC_001416‑4 | 8,328 | A→G | 100% | H149H (CAT→CAC) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,342 | C→T | 100% | V145I (GTT→ATT) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,442 | G→A | 100% | N111N (AAC→AAT) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,514 | G→A | 100% | I87I (ATC→ATT) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,559 | G→A | 100% | N72N (AAC→AAT) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,597 | C→T | 100% | D60N (GAC→AAC) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,708 | T→C | 100% | T23A (ACG→GCG) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,728 | C→T | 100% | R16K (AGG→AAG) | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,774 | C→A | 100% | M1M (GTG→TTG) † | lambdap78 ← | putative envelope protein |
| RA | NC_001416‑4 | 8,868 | T→C | 100% | intergenic (‑94/‑69) | lambdap78 ← / → lambdap79 | putative envelope protein/hypothetical protein |
| RA | NC_001416‑4 | 9,077 | A→G | 100% | R47R (AGA→AGG) | lambdap79 → | hypothetical protein |
| RA | NC_001416‑4 | 9,172 | T→C | 100% | intergenic (+29/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,176 | 2 bp→AC | 100% | intergenic (+33/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,314 | T→A | 5.7% | intergenic (+171/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,323 | T→C | 6.1% | intergenic (+180/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,325 | T→G | 7.2% | intergenic (+182/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,326 | A→G | 6.1% | intergenic (+183/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,359 | T→C | 82.1% | intergenic (+216/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,401 | G→A | 15.1% | intergenic (+258/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,494 | C→A | 15.2% | intergenic (+351/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,626 | C→G | 8.8% | intergenic (+483/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,628 | C→A | 8.8% | intergenic (+485/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,629 | C→G | 11.2% | intergenic (+486/–) | lambdap79 → / – | hypothetical protein/– |
| RA | NC_001416‑4 | 9,631 | C→T | 11.2% | intergenic (+488/–) | lambdap79 → / – | hypothetical protein/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_001416‑0 | 1 | 2 | 2 | NA [0] | [0] 157 | –/nu1 | –/DNA packaging protein |
| * | * | ÷ | NC_001416‑4 | 9652 | 9701 | 50 | 43 [42] | [0] NA | lambdap79/– | hypothetical protein/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_001416‑0 | = 9700 | 0 (0.000) | 119 (1.660) | 35/48 | NT | 100% | intergenic (+5/–) | V/– | tail component/– |
| ? | NC_001416‑1 | 1 = | 0 (0.000) | intergenic (–/‑10) | –/G | –/tail component | |||||
| * | ? | NC_001416‑1 | = 9700 | 0 (0.000) | 69 (0.940) | 32/48 | NT | 100% | coding (436/436 nt) | lom | outer host membrane |
| ? | NC_001416‑2 | 1 = | 0 (0.000) | intergenic (–/‑249) | –/orf‑401 | –/Tail fiber protein | |||||
| * | ? | NC_001416‑2 | = 9701 | 0 (0.000) | 38 (0.440) | 20/48 | NT | 100% | intergenic (‑23/–) | xis/– | Excisionase/– |
| ? | NC_001416‑3 | 1 = | 0 (0.000) | intergenic (–/+16) | –/lambdap35 | –/hypothetical protein | |||||
| * | ? | NC_001416‑3 | = 9700 | 0 (0.000) | 114 (1.200) | 38/48 | NT | 100% | coding (116/116 nt) | O | DNA replication protein |
| ? | NC_001416‑4 | 1 = | 0 (0.000) | intergenic (–/‑780) | –/P | –/DNA replication protein | |||||