mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 44,293 | Δ1 bp | 100% | intergenic (+124/‑367) | oprD_1 → / → czcR_2 | Porin D/Transcriptional activator protein CzcR |
| RA | 79,227 | T→A | 5.9% | D175V (GAC→GTC) | betC ← | Choline‑sulfatase |
| RA | 120,975 | Δ1 bp | 100% | intergenic (+272/+100) | polA → / ← engB | DNA polymerase I/putative GTP‑binding protein EngB |
| RA | 179,484 | T→C | 100% | C316R (TGC→CGC) | CJ019_00182 → | hypothetical protein |
| RA | 193,160 | T→A | 16.2% | N2673K (AAT→AAA) | CJ019_00185 → | hypothetical protein |
| RA | 255,173 | T→A | 5.7% | V203E (GTG→GAG) | CJ019_00230 → | hypothetical protein |
| RA | 445,359 | A→G | 73.8% | H76R (CAC→CGC) | argD_1 → | Acetylornithine aminotransferase |
| RA | 464,249 | A→G | 16.0% | V579A (GTG→GCG) | rpoD ← | RNA polymerase sigma factor RpoD |
| RA | 465,344 | C→T | 63.1% | G214D (GGC→GAC) | rpoD ← | RNA polymerase sigma factor RpoD |
| RA | 570,448 | A→C | 34.6% | D599A (GAC→GCC) | fdoG_2 → | Formate dehydrogenase‑O major subunit |
| RA | 605,516 | C→T | 8.6% | A572A (GCG→GCA) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| RA | 616,680 | G→T | 14.3% | T17T (ACC→ACA) | CJ019_00584 ← | hypothetical protein |
| RA | 687,469 | C→A | 6.4% | P87Q (CCA→CAA) | CJ019_00644 → | Omega‑amino acid‑‑pyruvate aminotransferase |
| RA | 690,144 | A→G | 100% | intergenic (+21/‑2438) | bauC → / → PP_RS08750 | Putative 3‑oxopropanoate dehydrogenase/tRNA‑Val |
| RA | 935,998 | A→C | 26.2% | F892V (TTC→GTC) | CJ019_00881 ← | hypothetical protein |
| RA | 1,176,644 | C→A | 7.2% | G265V (GGC→GTC) | mltF_1 ← | Membrane‑bound lytic murein transglycosylase F |
| RA | 1,227,173 | A→G | 67.7% | V389A (GTC→GCC) | glpK ← | Glycerol kinase |
| RA | 1,287,317 | C→A | 5.2% | A37S (GCA→TCA) | CJ019_01209 ← | hypothetical protein |
| RA | 1,312,593 | A→G | 100% | Q255R (CAG→CGG) | aaeA_2 → | p‑hydroxybenzoic acid efflux pump subunit AaeA |
| RA | 1,346,999 | A→G | 100% | R477R (CGT→CGC) | CJ019_01261 ← | hypothetical protein |
| RA | 1,385,093 | T→G | 17.7% | intergenic (+71/‑44) | aspS → / → pmpR | Aspartate‑‑tRNA(Asp/Asn) ligase/Transcriptional regulatory protein PmpR |
| RA | 1,456,028 | A→C | 15.5% | intergenic (‑50/+92) | patA ← / ← algL | Peptidoglycan O‑acetyltransferase/Alginate lyase |
| RA | 1,630,540 | A→C | 27.6% | L419R (CTG→CGG) | czcS ← | Sensor protein CzcS |
| RA | 1,673,889 | T→G | 19.3% | intergenic (‑33/‑98) | smtB ← / → yaeQ | Succinyl‑CoA‑‑L‑malate CoA‑transferase betasubunit/putative protein YaeQ |
| RA | 1,686,855 | C→G | 35.1% | L90V (CTG→GTG) | CJ019_01584 → | hypothetical protein |
| RA | 1,735,045 | T→C | 69.6% | intergenic (‑77/+7) | CJ019_01633 ← / ← CJ019_01634 | hypothetical protein/hypothetical protein |
| RA | 1,986,661 | A→C | 44.5% | intergenic (+42/+56) | mshA_1 → / ← CJ019_01891 | D‑inositol‑3‑phosphate glycosyltransferase/hypothetical protein |
| RA | 2,020,866:1 | +C | 100% | coding (599/1005 nt) | tagO → | putative undecaprenyl‑phosphateN‑acetylglucosaminyl 1‑phosphate transferase |
| RA | 2,041,924 | T→G | 35.4% | intergenic (+106/+33) | yfcG_2 → / ← CJ019_01936 | Disulfide‑bond oxidoreductase YfcG/hypothetical protein |
| RA | 2,094,808 | A→C | 34.9% | L186R (CTG→CGG) | CJ019_01995 ← | hypothetical protein |
| RA | 2,094,817 | T→G | 30.5% | Q183P (CAG→CCG) | CJ019_01995 ← | hypothetical protein |
| RA | 2,171,262 | C→A | 11.9% | F147L (TTC→TTA) | CJ019_02060 → | IS1182 family transposase ISPpu16 |
| JC | 2,191,046 | +CTGAAAATATCTCTTAT | 100% | intergenic (‑1/‑313) | PP_RS10045 ← / → purU_3 | LysR family transcriptional regulator/Formyltetrahydrofolate deformylase |
| RA | 2,332,171 | C→T | 5.9% | A308A (GCC→GCT) | ybhH → | Putative isomerase YbhH |
| RA | 2,491,259 | A→C | 33.3% | A34A (GCA→GCC) | iutA → | Ferric aerobactin receptor |
| RA | 2,703,424 | T→C | 12.0% | R321R (CGT→CGC) | CJ019_02554 → | hypothetical protein |
| RA | 2,737,398 | G→C | 33.8% | Q241H (CAG→CAC) | CJ019_02580 → | hypothetical protein |
| RA | 2,793,849 | A→G | 12.9% | E51G (GAA→GGA) | rbsB → | Ribose import binding protein RbsB |
| RA | 3,013,661 | G→A | 5.3% | A387T (GCG→ACG) | bcsC → | Cellulose synthase operon protein C |
| RA | 3,052,174 | T→C | 7.4% | L138P (CTG→CCG) | CJ019_02867 → | hypothetical protein |
| RA | 3,181,018 | G→A | 100% | A532T (GCC→ACC) | actP_2 → | Cation/acetate symporter ActP |
| RA | 3,267,793 | T→G | 23.0% | L171V (TTG→GTG) | eamA → | putative amino‑acid metabolite efflux pump |
| RA | 3,427,762 | T→G | 24.4% | F77V (TTC→GTC) | CJ019_03251 → | hypothetical protein |
| RA | 3,440,326 | A→C | 49.7% | S18R (AGC→CGC) | CJ019_03266 → | hypothetical protein |
| RA | 3,660,726 | T→G | 19.4% | D334A (GAC→GCC) | CJ019_03469 ← | putative protein |
| RA | 3,784,646 | T→G | 35.2% | D571A (GAC→GCC) | dmdC_4 ← | 3‑methylmercaptopropionyl‑CoA dehydrogenase |
| RA | 3,861,137 | C→A | 6.7% | R142R (CGC→CGA) | CJ019_03659 → | Gluconokinase |
| RA | 3,861,411 | A→G | 6.7% | T17A (ACC→GCC) | gntT_2 → | High‑affinity gluconate transporter |
| RA | 3,969,743 | A→C | 51.1% | A251A (GCT→GCG) | CJ019_03750 ← | putative protein |
| RA | 4,037,737 | A→G | 6.3% | I88V (ATT→GTT) | rhtB_3 → | Homoserine/homoserine lactone efflux protein |
| RA | 4,091,127 | C→T | 7.0% | R59R (CGG→CGA) | dmlR_15 ← | HTH‑type transcriptional regulator DmlR |
| RA | 4,135,590 | A→C | 27.0% | Q32P (CAG→CCG) | tgnC → | (Z)‑2‑((N‑methylformamido)methylene)‑5‑hydroxybu tyrolactone dehydrogenase |
| RA | 4,190,676 | G→A | 100% | intergenic (+890/+101) | CJ019_03940 → / ← CJ019_03941 | hypothetical protein/hypothetical protein |
| RA | 4,245,128 | A→C | 38.7% | L178R (CTG→CGG) | CJ019_03982 ← | Crotonyl‑CoA hydratase |
| JC | 4,257,334 | +CGCGGCCG | 100% | intergenic (‑280/+8) | CJ019_03991 ← / ← CJ019_03994 | putative ABC transporter ATP‑binding protein/hypothetical protein |
| RA | 4,263,673 | C→T | 5.4% | C117Y (TGC→TAC) | CJ019_03998 ← | hypothetical protein |
| RA | 4,294,789 | G→T | 7.5% | Q371K (CAG→AAG) | soxA_2 ← | Monomeric sarcosine oxidase |
| RA | 4,325,308 | C→T | 5.2% | P162P (CCG→CCA) | CJ019_04061 ← | hypothetical protein |
| RA | 4,341,972 | G→A | 8.9% | P242L (CCG→CTG) | tsdA ← | Thiosulfate dehydrogenase |
| RA | 4,472,981 | T→C | 6.1% | L418P (CTG→CCG) | hcaB_2 → | 3‑phenylpropionate‑dihydrodiol/cinnamicacid‑dihy d rodiol dehydrogenase |
| RA | 4,653,487 | A→T | 6.3% | N251I (AAC→ATC) | nuoG → | NADH‑quinone oxidoreductase subunit G |
| RA | 4,713,494 | Δ2 bp | 100% | coding (1668‑1669/1905 nt) | htpG ← | Chaperone protein HtpG |
| RA | 4,729,452 | C→T | 5.5% | V173M (GTG→ATG) | sdhA_2 ← | Succinate dehydrogenase flavoprotein subunit |
| RA | 4,749,727 | C→T | 100% | S441S (AGC→AGT) | ttgI_4 → | Toluene efflux pump outer membrane protein TtgI |
| RA | 4,759,509 | G→A | 100% | intergenic (+124/‑16) | fpvA_3 → / → ligM_KToptimized | Ferripyoverdine receptor/sequence generated by OPTIMIZER for KT2440 |
| RA | 4,882,564 | G→T | 5.9% | Q159H (CAG→CAT) | hyi → | Hydroxypyruvate isomerase |
| RA | 5,345,605 | G→A | 100% | Q611* (CAG→TAG) | pnp ← | Polyribonucleotide nucleotidyltransferase |
| RA | 5,386,500 | C→A | 100% | intergenic (‑509/+1142) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,503 | C→G | 100% | intergenic (‑512/+1139) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,506 | 1 bp→GT | 100% | intergenic (‑515/+1136) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,507:1 | +C | 100% | intergenic (‑516/+1135) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,510 | 2 bp→TA | 100% | intergenic (‑519/+1131) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,512:1 | +AA | 100% | intergenic (‑521/+1130) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,514 | T→C | 100% | intergenic (‑523/+1128) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,517 | G→C | 100% | intergenic (‑526/+1125) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,519 | G→A | 100% | intergenic (‑528/+1123) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,811 | C→T | 100% | intergenic (‑820/+831) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| MC JC | 5,390,395 | (CGCAT)2→1 | 100% | coding (489‑493/1666 nt) | ligH → | 10‑formyltetrahydrofolate synthetase |
| JC | 5,391,707 | +54 bp | 100% | intergenic (+124/‑1253) | ligH → / → CJ019_05072 | 10‑formyltetrahydrofolate synthetase/hypothetical protein |
| RA | 5,454,155 | C→A | 5.2% | F234L (TTC→TTA) | leuS → | Leucine‑‑tRNA ligase |
| RA | 5,507,090 | T→G | 53.3% | L35R (CTG→CGG) | CJ019_05179 → | hypothetical protein |
| RA | 5,693,175 | A→C | 48.0% | S236R (AGC→CGC) | pyrC' → | Dihydroorotase‑like protein |
| RA | 5,693,183 | T→G | 58.2% | R238R (CGT→CGG) | pyrC' → | Dihydroorotase‑like protein |
| RA | 5,760,593 | Δ1 bp | 100% | coding (776/834 nt) | CJ019_05400 → | hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | ACB143 | 82194 | 82364 | 171 | 19 [18] | [18] 19 | trpA | Tryptophan synthase alpha chain |
| * | * | ÷ | ACB143 | 161221 | 161417–161315 | 95–197 | 19 [14] | [16] 19 | [uctC_1] | [uctC_1] |
| * | * | ÷ | ACB143 | 517190 | 517290 | 101 | 20 [12] | [18] 19 | tyrS/birA | Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA |
| * | * | ÷ | ACB143 | 674250 | 674380 | 131 | 19 [16] | [11] 19 | [nimR_1]–[mcpH_2] | [nimR_1],[mcpH_2] |
| * | * | ÷ | ACB143 | 1396585 | 1396672 | 88 | 20 [18] | [16] 21 | [CJ019_01313]–[mcpU_1] | [CJ019_01313],[mcpU_1] |
| * | * | ÷ | ACB143 | 1422665–1423227 | 1424408–1423230 | 4–1744 | 19 [15] | [18] 19 | [CJ019_01343]–[CJ019_01346] | [CJ019_01343],[CJ019_01346] |
| * | * | ÷ | ACB143 | 1457225 | 1457312 | 88 | 19 [18] | [18] 21 | [algX] | [algX] |
| * | * | ÷ | ACB143 | 1492489 | 1492581 | 93 | 19 [18] | [13] 19 | CJ019_01406/zapE_1 | hypothetical protein/Cell division protein ZapE |
| * | * | ÷ | ACB143 | 1585618 | 1585706 | 89 | 19 [18] | [18] 19 | CJ019_01493 | hypothetical protein |
| * | * | ÷ | ACB143 | 1608679 | 1608801 | 123 | 20 [17] | [18] 20 | CJ019_01513 | hypothetical protein |
| * | * | ÷ | ACB143 | 1697643 | 1697741 | 99 | 26 [18] | [18] 19 | [CJ019_01593] | [CJ019_01593] |
| * | * | ÷ | ACB143 | 1705075 | 1705214 | 140 | 19 [18] | [17] 20 | ppc/adk | Phosphoenolpyruvate carboxylase/Adenylate kinase |
| * | * | ÷ | ACB143 | 2288820 | 2288927 | 108 | 19 [18] | [16] 20 | [CJ019_02172] | [CJ019_02172] |
| * | * | ÷ | ACB143 | 2830079 | 2830221 | 143 | 20 [18] | [14] 19 | [gabD1] | [gabD1] |
| * | * | ÷ | ACB143 | 3046173 | 3046328 | 156 | 19 [18] | [18] 19 | [rcsC_5]–[degU_2] | [rcsC_5],[degU_2] |
| * | * | ÷ | ACB143 | 4163761 | 4163856 | 96 | 26 [17] | [17] 22 | katG/leuO_2 | Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO |
| * | * | ÷ | ACB143 | 4344747 | 4344859 | 113 | 19 [17] | [17] 19 | nmoA | Nitronate monooxygenase |
| * | * | ÷ | ACB143 | 4732396 | 4732518 | 123 | 19 [18] | [16] 20 | [CJ019_04468] | [CJ019_04468] |
| * | * | ÷ | ACB143 | 4845696 | 4845936 | 241 | 19 [18] | [18] 19 | recR/ybaB | Recombination protein RecR/Nucleoid‑associated protein YbaB |
| * | * | ÷ | ACB143 | 5192928 | 5193062 | 135 | 25 [16] | [18] 19 | [gltR_4]–[CJ019_04888] | [gltR_4],[CJ019_04888] |
| * | * | ÷ | ACB143 | 5250102 | 5250240 | 139 | 20 [15] | [17] 21 | [CJ019_04947]–[CJ019_04948] | [CJ019_04947],[CJ019_04948] |
| * | * | ÷ | ACB143 | 5503618 | 5503856 | 239 | 19 [16] | [18] 20 | [CJ019_05176] | [CJ019_05176] |
| * | * | ÷ | ACB143 | 5534191 | 5534310 | 120 | 19 [18] | [17] 19 | [nadE] | [nadE] |
| * | * | ÷ | ACB143 | 5678523 | 5678661 | 139 | 21 [18] | [14] 22 | CJ019_05328/CJ019_05329 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 5900295 | 5900397 | 103 | 20 [18] | [16] 20 | [CJ019_05521] | [CJ019_05521] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | ACB143 | 1837190 = | 0 (0.000) | 43 (0.740) | 22/232 | NT | 41.0% | coding (660/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | = 2172433 | 124 (2.140) | intergenic (+175/+93) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein | |||||
| * | ? | ACB143 | = 1837193 | 0 (0.000) | 31 (0.530) | 27/234 | NT | 51.2% | coding (657/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | 2170759 = | 59 (1.010) | intergenic (‑774/‑63) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 | |||||
| * | ? | ACB143 | 2155685 = | 60 (0.990) | 70 (1.160) | 32/242 | NT | 53.8% | coding (301/369 nt) | tmk_1 | Thymidylate kinase |
| ? | ACB143 | = 2220562 | 60 (0.990) | coding (36/369 nt) | tmk_2 | Thymidylate kinase | |||||
| * | ? | ACB143 | 2170758 = | 59 (0.980) | 42 (0.710) | 26/238 | NT | 59.1% | intergenic (‑773/‑64) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | 5563630 = | 0 (0.000) | coding (1047/1902 nt) | mutL_2 | DNA mismatch repair protein MutL | |||||
| * | ? | ACB143 | = 2172434 | 124 (2.050) | 34 (0.570) | 21/240 | NT | 35.6% | intergenic (+176/+92) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | = 5563631 | 0 (0.000) | coding (1046/1902 nt) | mutL_2 | DNA mismatch repair protein MutL | |||||
| * | ? | ACB143 | = 2930727 | 4 (0.070) | 39 (0.660) | 19/238 | NT | 90.8% | intergenic (+44/+39) | nanT_2/CJ019_02768 | Sialic acid transporter NanT/IS110 family transposase ISPpu9 |
| ? | ACB143 | 3819889 = | NA (NA) | intergenic (‑13/+386) | CJ019_03622/CJ019_02768 | IS110 family transposase ISPpu9/IS110 family transposase ISPpu9 | |||||
| * | ? | ACB143 | 3359593 = | 35 (0.580) | 73 (1.210) | 44/242 | NT | 80.7% | intergenic (+219/‑151) | pikAII_1/CJ019_03160 | Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42 |
| ? | ACB143 | 5775225 = | 0 (0.000) | coding (1544/2151 nt) | CJ019_05409 | hypothetical protein | |||||
| * | ? | ACB143 | = 3376605 | 56 (0.930) | 56 (0.930) | 35/240 | NT | 66.9% | coding (501/546 nt) | CJ019_03184 | hypothetical protein |
| ? | ACB143 | = 5775229 | 0 (0.000) | coding (1540/2151 nt) | CJ019_05409 | hypothetical protein | |||||