mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 547,694 | A→G | E38E (GAA→GAG) | Y75_RS02655 → | hypothetical protein |
| RA | 547,835 | +G | coding (255/261 nt) | Y75_RS02655 → | hypothetical protein |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| MC JC | 654,214 | Δ1,199 bp | Y75_RS03225–[dcuC] | Y75_RS03225, [dcuC] | |
| RA | 909,411 | G→A | P102P (CCC→CCT) | ltaE ← | low‑specificity L‑threonine aldolase |
| RA | 987,574 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | porin OmpF/asparagine‑‑tRNA ligase |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | Y75_RS05355 → | GGDEF domain‑containing protein |
| RA | 1,197,797 | C→T | H366H (CAC→CAT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,809 | C→T | T370T (ACC→ACT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| MC JC | 1,301,041 | Δ1,336 bp | Y75_RS06530–Y75_RS06530 | Y75_RS06530, Y75_RS06530 | |
| RA | 1,337,160 | G→A | Q52Q (CAG→CAA) | Y75_RS06715 → | hypothetical protein |
| RA | 1,485,978 | C→A | R402S (CGT→AGT) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,519,222 | G→T | V40V (GTG→GTT) | Y75_RS07640 → | orphan toxin OrtT |
| RA | 1,553,904 | 2 bp→CT | intergenic (+199/+207) | fdnI → / ← Y75_RS07795 | formate dehydrogenase‑N subunit gamma/HigA family addiction module antidote protein |
| RA | 1,553,926 | T→C | intergenic (+221/+186) | fdnI → / ← Y75_RS07795 | formate dehydrogenase‑N subunit gamma/HigA family addiction module antidote protein |
| RA | 1,592,479 | C→A | intergenic (‑223/+89) | Y75_RS07945 ← / ← hipA | helix‑turn‑helix transcriptional regulator/type II toxin‑antitoxin system serine/threonine protein kinase toxin HipA |
| RA | 1,669,601 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,704,037 | Δ1 bp | coding (91/1002 nt) | add → | adenosine deaminase |
| RA | 1,979,957 | G→T | intergenic (‑46/+398) | flhD ← / ← Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase |
| RA | 2,005,401 | C→T | E115K (GAA→AAA) | fliC ← | H48 family flagellin FliC |
| RA | 2,156,723 | C→A | L191M (CTG→ATG) | mdtA → | multidrug efflux RND transporter subunit MdtA |
| MC JC | 2,176,983 | Δ1,199 bp | Y75_RS10980–[gatA] | Y75_RS10980, [gatA] | |
| RA | 2,245,455 | A→G | S283P (TCG→CCG) | Y75_RS11290 ← | DUF418 family protein |
| MC JC | 2,320,795 | Δ1,336 bp | Y75_RS11650–[rcsC] | Y75_RS11650, Y75_RS11650, [rcsC] | |
| RA | 2,447,095 | C→T | intergenic (‑44/‑115) | fabB ← / → mnmC | beta‑ketoacyl‑ACP synthase I/bifunctional tRNA (5‑methylaminomethyl‑2‑thiouridine)(34)‑methyltransferase MnmD/FAD‑dependent 5‑carboxymethylaminomethyl‑2‑thiouridine(34) oxidoreductase MnmC |
| RA | 2,866,111 | A→G | pseudogene (97/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,104,794 | G→A | G142D (GGC→GAC) | Y75_RS15435 → | nucleoside permease |
| RA | 3,212,340 | A→C | D213A (GAC→GCC) | rpoD → | RNA polymerase sigma factor RpoD |
| MC JC | 3,261,134 | Δ1,199 bp | Y75_RS16205–[tdcD] | Y75_RS16205, [tdcD] | |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | Y75_RS16240 → | YhaC family protein |
| MC JC | 3,742,936 | Δ1,336 bp | Y75_RS18560–Y75_RS18560 | Y75_RS18560, Y75_RS18560 | |
| MC JC | 3,746,911 | Δ1,199 bp | Y75_RS18585–[tnaB] | Y75_RS18585, [tnaB] | |
| MC JC | 3,750,591 | Δ1,199 bp | Y75_RS18600 | Y75_RS18600 | |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | Y75_RS19595 → | C4‑dicarboxylate transporter DctC |
| MC JC | 3,974,646 | Δ78 bp | coding (42‑119/825 nt) | gadX → | acid resistance transcriptional activator GadX |
| RA | 4,114,118 | C→A | intergenic (‑171/‑149) | igaA ← / → nudE | intracellular growth attenuator protein IgaA/ADP compounds hydrolase NudE |
| MC JC | 4,310,363 | Δ1,199 bp | Y75_RS21310–[alsK] | Y75_RS21310, [alsK] | |
| RA | 4,371,274 | (A)5→3 | pseudogene (179‑180/1304 nt) | Y75_RS21600 ← | anaerobic C4‑dicarboxylate transporter |
| RA | 4,397,126 | Δ1 bp | intergenic (+11/‑26) | Y75_RS21735 → / → Y75_RS21740 | tRNA‑Gly/tRNA‑Gly |
| RA | 4,397,133 | C→T | intergenic (+18/‑19) | Y75_RS21735 → / → Y75_RS21740 | tRNA‑Gly/tRNA‑Gly |
| RA | 4,397,136 | A→G | intergenic (+21/‑16) | Y75_RS21735 → / → Y75_RS21740 | tRNA‑Gly/tRNA‑Gly |
| RA | 4,405,094 | G→A | V43M (GTG→ATG) | hfq → | RNA chaperone Hfq |
| RA | 4,470,927 | G→A | intergenic (‑67/+52) | treB ← / ← treR | PTS trehalose transporter subunit IIBC/trehalose operon repressor |
| RA | 4,639,891 | A→G | S34P (TCC→CCC) | robA ← | MDR efflux pump AcrAB transcriptional activator RobA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 683144 | 689347–688274 | 5131–6204 | 147 [0] | [63] 64 | [Y75_RS03375]–[Y75_RS03405] | [Y75_RS03375],rihA,gltL,gltK,gltJ,gltI,[Y75_RS03405] |
| * | * | ÷ | NC_007779 | 1197822 | 1213084 | 15263 | 65 [63] | [63] 64 | [icd]–[Y75_RS23470] | [icd],Y75_RS05945,Y75_RS05950,lit,Y75_RS05960,Y75_RS05965,Y75_RS24820,Y75_RS23460,Y75_RS05970,Y75_RS05975,Y75_RS05980,ymfL,Y75_RS23465,Y75_RS05995,Y75_RS06000,Y75_RS06005,Y75_RS06010,Y75_RS06015,Y75_RS06020,Y75_RS06025,Y75_RS06030,Y75_RS06035,pinE,Y75_RS06045,[Y75_RS23470] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 380484 = | NA (NA) | 133 (1.140) | 117/496 | 0.1 | NA | coding (28/444 nt) | Y75_RS01845 | transferase |
| ? | NC_007779 | = 381407 | NA (NA) | coding (518/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | 381401 = | NA (NA) | 85 (0.730) | 74/492 | 1.4 | NA | coding (512/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381812 | NA (NA) | pseudogene (174/174 nt) | Y75_RS23175 | acetyltransferase | |||||
| * | ? | NC_007779 | = 683143 | 0 (0.000) | 139 (1.200) | 111/494 | 0.1 | 100% | coding (673/1671 nt) | Y75_RS03375 | molecular chaperone HscC |
| ? | NC_007779 | 688274 = | NA (NA) | intergenic (‑105/+145) | gltI/Y75_RS03405 | glutamate/aspartate ABC transporter substrate‑binding protein GltI/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 1398952 | NA (NA) | 114 (0.980) | 98/496 | 0.3 | 98.3% | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NC_007779 | 1574188 = | 2 (0.020) | coding (2729/2796 nt) | Y75_RS07885 | insulinase family protein | |||||
| * | ? | NC_007779 | = 1574191 | 3 (0.030) | 142 (1.220) | 109/496 | 0.1 | 97.9% | coding (2726/2796 nt) | Y75_RS07885 | insulinase family protein |
| ? | NC_007779 | 2176983 = | NA (NA) | intergenic (‑3/‑32) | gatA/Y75_RS10980 | PTS galactitol transporter subunit IIA/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | 1881541 = | 4 (0.030) | 130 (1.120) | 113/492 | 0.1 | 97.0% | coding (122/360 nt) | yeaR | DUF1971 domain‑containing protein |
| ? | NC_007779 | = 2521060 | NA (NA) | intergenic (+171/+29) | Y75_RS12570/Y75_RS12575 | IS4‑like element IS421 family transposase/sensor domain‑containing phosphodiesterase | |||||
| * | ? | NC_007779 | = 1881551 | 3 (0.030) | 108 (0.940) | 94/490 | 0.4 | 97.3% | coding (112/360 nt) | yeaR | DUF1971 domain‑containing protein |
| ? | NC_007779 | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/Y75_RS12570 | nucleoside permease NupC/IS4‑like element IS421 family transposase | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 121 (1.040) | 105/494 | 0.2 | 99.2% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 1 (0.010) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | = 3512759 | 1 (0.010) | 99 (0.850) | 85/494 | 0.8 | 99.0% | coding (535/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR |
| ? | NC_007779 | = 3744262 | NA (NA) | intergenic (‑45/+31) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ | |||||
| * | ? | NC_007779 | = 3744263 | NA (NA) | 113 (0.970) | 96/496 | 0.4 | 98.3% | intergenic (‑46/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 2 (0.020) | coding (37/825 nt) | Y75_RS19350 | protein bax | |||||
| * | ? | NC_007779 | = 3903279 | 3 (0.030) | 123 (1.060) | 105/494 | 0.2 | 97.6% | coding (42/825 nt) | Y75_RS19350 | protein bax |
| ? | NC_007779 | = 4504190 | NA (NA) | intergenic (+10/+167) | Y75_RS22280/Y75_RS22285 | IS3‑like element IS2 family transposase/phosphoethanolamine transferase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 110 (0.940) | 93/496 | 0.5 | 98.2% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 4485284 = | 2 (0.020) | coding (875/1197 nt) | Y75_RS22200 | DUF898 domain‑containing protein | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 107 (0.920) | 92/494 | 0.5 | 95.5% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 5 (0.040) | intergenic (+204/+379) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 4311557 | NA (NA) | 140 (1.200) | 109/496 | 0.1 | 99.3% | pseudogene (921/921 nt) | alsK | allose kinase |
| ? | NC_007779 | = 4485287 | 1 (0.010) | coding (878/1197 nt) | Y75_RS22200 | DUF898 domain‑containing protein | |||||