mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 226,969 | G→A | noncoding (360/1542 nt) | ECD_RS01035 → | 16S ribosomal RNA |
| RA | 405,802 | G→T | T234K (ACG→AAG) | ispA ← | (2E,6E)‑farnesyl diphosphate synthase |
| RA | 519,071 | G→A | T100T (ACG→ACA) | ylbF → | DUF2877 domain‑containing protein |
| RA | 537,641 | G→A | G49R (GGA→AGA) | ybcK → | recombinase family protein |
| RA | 550,505 | G→T | intergenic (+14/‑45) | ECD_RS02675 → / → ECD_RS02680 | phage tail tip protein/prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,507 | Δ1 bp | intergenic (+16/‑43) | ECD_RS02675 → / → ECD_RS02680 | phage tail tip protein/prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,515 | C→T | intergenic (+24/‑35) | ECD_RS02675 → / → ECD_RS02680 | phage tail tip protein/prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,524 | G→A | intergenic (+33/‑26) | ECD_RS02675 → / → ECD_RS02680 | phage tail tip protein/prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,663 | G→A | pseudogene (114/364 nt) | ECD_RS02680 → | prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,708 | T→C | pseudogene (159/364 nt) | ECD_RS02680 → | prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,712 | C→T | pseudogene (163/364 nt) | ECD_RS02680 → | prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,798 | A→T | pseudogene (249/364 nt) | ECD_RS02680 → | prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,888 | G→A | pseudogene (339/364 nt) | ECD_RS02680 → | prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,900 | C→T | pseudogene (351/364 nt) | ECD_RS02680 → | prophage tail fiber N‑terminal domain‑containing protein |
| RA | 550,927 | G→A | intergenic (+14/+71) | ECD_RS02680 → / ← ECD_RS02685 | prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein |
| RA | 550,939 | C→A | intergenic (+26/+59) | ECD_RS02680 → / ← ECD_RS02685 | prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein |
| RA | 550,945 | T→A | intergenic (+32/+53) | ECD_RS02680 → / ← ECD_RS02685 | prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein |
| RA | 550,988 | A→C | intergenic (+75/+10) | ECD_RS02680 → / ← ECD_RS02685 | prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein |
| RA | 642,526 | A→T | K5* (AAA→TAA) | ECD_RS25105 → | IS3‑like element IS150 family transposase |
| MC JC | 748,650 | Δ4,449 bp | lacI–[ECD_RS03715] | lacI, ECD_RS03705, ECD_RS03710, [ECD_RS03715] | |
| RA | 753,173 | G→A | pseudogene (831/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,248 | T→C | pseudogene (756/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,262 | T→C | pseudogene (742/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,271 | C→T | pseudogene (733/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,513 | T→G | pseudogene (491/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,674 | A→C | pseudogene (330/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,778 | A→G | pseudogene (226/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 753,860 | A→G | pseudogene (144/921 nt) | ECD_RS03715 ← | phage integrase Arm DNA‑binding domain‑containing protein |
| RA | 754,025 | C→T | G59S (GGC→AGC) | ECD_RS03720 ← | excisionase |
| RA | 754,080 | C→T | E40E (GAG→GAA) | ECD_RS03720 ← | excisionase |
| RA | 754,104 | T→A | P32P (CCA→CCT) | ECD_RS03720 ← | excisionase |
| RA | 754,122 | C→G | R26R (CGG→CGC) | ECD_RS03720 ← | excisionase |
| RA | 754,125 | A→C | V25V (GTT→GTG) | ECD_RS03720 ← | excisionase |
| RA | 754,158 | A→G | R14R (CGT→CGC) | ECD_RS03720 ← | excisionase |
| RA | 754,170 | T→A | A10A (GCA→GCT) | ECD_RS03720 ← | excisionase |
| RA | 754,247 | C→A | A54S (GCC→TCC) | ECD_RS03725 ← | hypothetical protein |
| RA | 754,286 | C→T | V41I (GTA→ATA) | ECD_RS03725 ← | hypothetical protein |
| RA | 754,371 | C→T | E12E (GAG→GAA) | ECD_RS03725 ← | hypothetical protein |
| RA | 754,386 | T→A | G7G (GGA→GGT) | ECD_RS03725 ← | hypothetical protein |
| RA | 762,867 | T→G | L169L (CTT→CTG) | ECD_RS03820 → | replication protein P |
| RA | 762,873 | T→C | D171D (GAT→GAC) | ECD_RS03820 → | replication protein P |
| RA | 762,885 | C→G | R175R (CGC→CGG) | ECD_RS03820 → | replication protein P |
| RA | 762,888 | T→C | R176R (CGT→CGC) | ECD_RS03820 → | replication protein P |
| RA | 762,894 | C→T | A178A (GCC→GCT) | ECD_RS03820 → | replication protein P |
| RA | 762,897 | A→C | A179A (GCA→GCC) | ECD_RS03820 → | replication protein P |
| RA | 762,903 | G→A | E181E (GAG→GAA) | ECD_RS03820 → | replication protein P |
| RA | 762,906 | Δ1 bp | coding (546/702 nt) | ECD_RS03820 → | replication protein P |
| RA | 762,911 | 1 bp→TG | coding (551/702 nt) | ECD_RS03820 → | replication protein P |
| RA | 762,918 | T→C | T186T (ACT→ACC) | ECD_RS03820 → | replication protein P |
| RA | 762,922 | A→C | R188R (AGA→CGA) | ECD_RS03820 → | replication protein P |
| RA | 762,945 | C→A | I195I (ATC→ATA) | ECD_RS03820 → | replication protein P |
| RA | 763,051 | G→T | A231S (GCA→TCA) | ECD_RS03820 → | replication protein P |
| RA | 763,103 | T→G | intergenic (+41/‑73) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,115 | G→A | intergenic (+53/‑61) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,117 | C→A | intergenic (+55/‑59) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,131 | C→G | intergenic (+69/‑45) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,139 | C→T | intergenic (+77/‑37) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,145 | A→C | intergenic (+83/‑31) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,166 | C→T | intergenic (+104/‑10) | ECD_RS03820 → / → ECD_RS03830 | replication protein P/metallophosphoesterase |
| RA | 763,181 | A→G | A2A (GCA→GCG) | ECD_RS03830 → | metallophosphoesterase |
| RA | 767,828 | A→C | K40Q (AAG→CAA) | ybcW → | protein YbcW |
| RA | 767,830 | G→A | K40Q (AAG→CAA) | ybcW → | protein YbcW |
| RA | 767,851 | A→G | R47R (AGA→AGG) | ybcW → | protein YbcW |
| RA | 767,863 | A→C | A51A (GCA→GCC) | ybcW → | protein YbcW |
| RA | 767,869 | G→A | L53L (TTG→TTA) | ybcW → | protein YbcW |
| RA | 767,872 | G→A | V54V (GTG→GTA) | ybcW → | protein YbcW |
| RA | 767,884 | T→G | N58K (AAT→AAG) | ybcW → | protein YbcW |
| RA | 767,889 | T→C | M60T (ATG→ACG) | ybcW → | protein YbcW |
| RA | 767,934 | T→C | intergenic (+17/+148) | ybcW → / ← ECD_RS03870 | protein YbcW/YlcI/YnfO family protein |
| RA | 791,198 | C→T | intergenic (‑628/+228) | ECD_RS03990 ← / ← ybhB | hypothetical protein/kinase inhibitor |
| RA | 791,250 | A→T | intergenic (‑680/+176) | ECD_RS03990 ← / ← ybhB | hypothetical protein/kinase inhibitor |
| RA | 855,155 | G→A | E90E (GAG→GAA) | gsiC → | glutathione ABC transporter permease GsiC |
| RA | 862,724 | T→C | S22P (TCT→CCT) | yliI → | aldose sugar dehydrogenase YliI |
| RA | 931,389 | G→T | S37S (TCC→TCA) | infA ← | translation initiation factor IF‑1 |
| RA | 992,215 | C→T | intergenic (‑143/+459) | ompF ← / ← asnS | porin OmpF/asparagine‑‑tRNA ligase |
| RA | 1,002,731 | G→A | intergenic (‑130/‑226) | ssuE ← / → elfA | NADPH‑dependent FMN reductase/fimbrial protein |
| RA | 1,026,045 | A→G | intergenic (‑37/‑182) | sulA ← / → sxy | SOS‑induced cell division inhibitor SulA/CRP‑S regulon transcriptional coactivator Sxy |
| RA | 1,100,143 | G→A | noncoding (76/88 nt) | ECD_RS05485 ← | tRNA‑Ser |
| RA | 1,137,851 | A→C | S186R (AGC→CGC) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,173,770 | G→A | L930F (CTT→TTT) | mfd ← | transcription‑repair coupling factor |
| RA | 1,308,529 | G→A | Q4* (CAA→TAA) | trpE ← | anthranilate synthase component I |
| RA | 1,384,274 | A→G | pseudogene (421/753 nt) | fnr ← | fumarate/nitrate reduction transcriptional regulator Fnr |
| RA | 1,527,829 | A→G | intergenic (‑303/+59) | gadB ← / ← pqqL | glutamate decarboxylase/M16 family metallopeptidase |
| RA | 1,544,449 | C→T | pseudogene (2536/2651 nt) | ECD_RS26055 ← | fimbria/pilus outer membrane usher protein |
| RA | 1,559,313 | C→T | R363Q (CGG→CAG) | ECD_RS07860 ← | diguanylate cyclase |
| RA | 1,814,885 | C→T | L42F (CTC→TTC) | cdgI → | GGDEF domain‑containing protein |
| RA | 1,822,910 | A→C | R273R (CGA→CGC) | dgcP → | diguanylate cyclase DgcP |
| RA | 1,834,871 | G→A | P201L (CCC→CTC) | fadD ← | long‑chain‑fatty‑acid‑‑CoA ligase FadD |
| RA | 1,949,161 | T→G | W122G (TGG→GGG) | mtfA → | DgsA anti‑repressor MtfA |
| RA | 1,973,596 | T→C | pseudogene (4/699 nt) pseudogene (144/144 nt) |
ECD_RS10050 ← ECD_RS25675 ← |
IS3‑like element IS2 family transposase putative zinc ribbon protein |
| RA | 2,007,879 | A→T | I247N (ATT→AAT) | wzx ← | O7 family O‑antigen flippase |
| MC JC | 2,068,532 | Δ776 bp | ECD_RS10480–[ECD_RS10485] | ECD_RS10480, ECD_RS10480, [ECD_RS10485] | |
| RA | 2,075,017 | A→C | intergenic (‑10/+290) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| JC | 2,135,130 | +GACAT | pseudogene (118/994 nt) | mglB ← | galactose/glucose ABC transporter substrate‑binding protein MglB |
| RA | 2,227,497 | 2 bp→AA | coding (2284‑2285/2628 nt) | gyrA ← | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| RA | 2,275,119 | 2 bp→TG | intergenic (+4/‑98) | ECD_RS25720 → / → yfbM | hypothetical protein/YfbM family protein |
| RA | 2,356,080 | C→T | L116L (CTG→TTG) | dsdX → | D‑serine transporter DsdX |
| RA | 2,477,975 | T→C | F532S (TTC→TCC) | hyfR → | DNA‑binding transcriptional regulator HyfR |
| MC JC | 2,517,851 | Δ1,445 bp | ECD_RS25300–ECD_RS25300 | ECD_RS25300, ECD_RS25300 | |
| RA | 2,567,019 | C→T | intergenic (‑223/+198) | shoB ← / ← acpS | type I toxin‑antitoxin system toxin ShoB/holo‑ACP synthase |
| RA | 2,764,352 | C→T | T236T (ACC→ACT) | xni → | flap endonuclease Xni |
| MC JC | 2,820,977 | Δ1,446 bp | [ECD_RS14045]–[ECD_RS14060] | [ECD_RS14045], ECD_RS25310, ECD_RS25310, [ECD_RS14060] | |
| RA | 2,879,376 | C→A | V175V (GTG→GTT) | gcvP ← | aminomethyl‑transferring glycine dehydrogenase |
| RA | 2,880,243 | C→T | D56N (GAT→AAT) | gcvH ← | glycine cleavage system protein GcvH |
| RA | 2,880,800 | T→C | T243A (ACC→GCC) | gcvT ← | glycine cleavage system aminomethyltransferase GcvT |
| RA | 2,891,803 | G→A | G32G (GGG→GGA) | scpA → | methylmalonyl‑CoA mutase |
| RA | 2,891,814 | A→C | K36T (AAG→ACG) | scpA → | methylmalonyl‑CoA mutase |
| RA | 2,900,353 | A→G | L105L (TTA→CTA) | mscS ← | small‑conductance mechanosensitive channel MscS |
| RA | 3,162,393 | C→T | L165L (CTC→CTT) | lpoA → | penicillin‑binding protein activator LpoA |
| RA | 3,197,975 | 2 bp→GT | coding (514‑515/1434 nt) | dacB → | serine‑type D‑Ala‑D‑Ala carboxypeptidase |
| RA | 3,443,292 | G→A | A221A (GCC→GCT) | yhhX ← | oxidoreductase |
| RA | 3,496,959 | C→T | intergenic (‑116/‑267) | ECD_RS17420 ← / → yhiM | YhiJ/YhiL family protein/DUF2776 domain‑containing protein |
| RA | 3,733,869 | T→G | H513Q (CAT→CAG) | adeD → | adenine deaminase |
| RA | 3,757,620 | G→A | L151L (CTC→CTT) | yidR ← | DUF3748 domain‑containing protein |
| RA | 3,817,054 | T→C | M451V (ATG→GTG) | viaA ← | ATPase RavA stimulator ViaA |
| MC JC | 3,822,341 | Δ1,441 bp | [rbsD]–[rbsD] | [rbsD], ECD_RS25390, ECD_RS25390, [rbsD] | |
| RA | 3,997,577 | A→G | F459F (TTT→TTC) | frvB ← | PTS fructose‑like transporter subunit IIBC |
| RA | 4,072,111 | T→C | pseudogene (172/1845 nt) | btuB → | TonB‑dependent vitamin B12 receptor BtuB |
| RA | 4,108,278 | C→T | intergenic (+132/‑55) | yjaG → / → hupA | YjaG family protein/nucleoid‑associated protein HU‑alpha |
| RA | 4,179,097 | Δ1 bp | coding (2184/2823 nt) | uvrA ← | excinuclease ABC subunit UvrA |
| RA | 4,395,355 | G→T | T108T (ACC→ACA) | holC ← | DNA polymerase III subunit chi |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_012971 | 543871–544403 | 549187 | 4785–5317 | 36 [34] | [0] 104 | [ECD_RS02625]–[ECD_RS02675] | [ECD_RS02625],ECD_RS02625,ECD_RS02630,essD,rrrD,rzpD,iss,ECD_RS02660,ECD_RS02670,[ECD_RS02675] |
| * | * | ÷ | NC_012971 | 550998 | 597471–596896 | 45899–46474 | 123 [0] | [35] 38 | [ECD_RS02685]–[ECD_RS02890] | [ECD_RS02685],cusS,cusR,cusC,cusF,cusB,cusA,pheP,ybdG,nfsB,ybdF,ybdJ,ybdK,ECD_RS25095,ECD_RS22975,ECD_RS22975,ECD_RS24565,hokE,ECD_RS02775,entD,fepA,fes,ybdZ,entF,wzz(fepE),fepC,fepG,fepD,entS,fepB,entC,entE,entB,entA,entH,cstA,ybdD,hcxA,ybdL,ybdM,ECD_RS02885,ECD_RS02890,[ECD_RS02890] |
| * | * | ÷ | NC_012971 | 754390 | 762860 | 8471 | 36 [35] | [7] 106 | [ECD_RS03725]–[ECD_RS03820] | [ECD_RS03725],ECD_RS03730,ECD_RS26520,ECD_RS03740,ECD_RS26465,ECD_RS03750,ECD_RS03755,ECD_RS03760,bet,ECD_RS03770,kil,ECD_RS25555,ECD_RS03785,ECD_RS03790,ECD_RS03795,ECD_RS03800,ECD_RS03805,ECD_RS03810,ECD_RS24605,[ECD_RS03820] |
| * | * | ÷ | NC_012971 | 763190 | 767804 | 4615 | 46 [31] | [33] 36 | [ECD_RS03830]–[ybcW] | [ECD_RS03830],ECD_RS03835,ECD_RS03840,ECD_RS03845,rzpD,bor,ybcV,[ybcW] |
| * | * | ÷ | NC_012971 | 767940 | 791180 | 23241 | 83 [0] | [31] 37 | ECD_RS03870–ECD_RS03990 | ECD_RS03870,ECD_RS03875,ECD_RS03880,ECD_RS03885,ECD_RS03890,ECD_RS03895,ECD_RS03900,ECD_RS03905,ECD_RS03910,ECD_RS03915,ECD_RS03920,ECD_RS03925,ECD_RS03930,gpG,ECD_RS03940,ECD_RS03945,ECD_RS03950,ECD_RS03955,ECD_RS03960,ECD_RS03965,gpJ,lom,ECD_RS23105,ECD_RS03990 |
| * | * | ÷ | NC_012971 | 1482315 | 1484648–1482389 | 75–2334 | 39 [33] | [34] 36 | [ECD_RS07535]–[ECD_RS23355] | [ECD_RS07535],[ECD_RS23355] |
| * | * | ÷ | NC_012971 | 3628743–3628880 | 3628944 | 65–202 | 36 [35] | [35] 36 | ECD_RS18025 | polymorphic toxin type 34 domain‑containing protein |
| * | * | ÷ | NC_012971 | 3944690–3945859 | 3946314–3946220 | 362–1625 | 36 [35] | [34] 36 | ECD_RS19585 | 23S ribosomal RNA |
| * | * | ÷ | NC_012971 | 4153661 | 4159658 | 5998 | 102 [0] | [0] 101 | [malE]–ECD_RS20580 | [malE],malK,lamB,malM,ECD_RS20580 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_012971 | = 536615 | 15 (0.150) | 99 (1.040) | 47/556 | 0.6 | 92.9% | pseudogene (1/228 nt) | ECD_RS02560 | protein ren |
| ? | NC_012971 | 762861 = | 1 (0.010) | coding (501/702 nt) | ECD_RS03820 | replication protein P | |||||
| * | ? | NC_012971 | 549188 = | 0 (0.000) | 104 (1.030) | 62/590 | 0.3 | 64.4% | pseudogene (506/1809 nt) | ECD_RS02675 | phage tail tip protein |
| ? | NC_012971 | 2827816 = | 115 (1.140) | coding (552/570 nt) | ECD_RS14080 | hypothetical protein | |||||
| * | ? | NC_012971 | = 550997 | 0 (0.000) | 123 (1.220) | 71/586 | 0.1 | 100% | intergenic (+84/+1) | ECD_RS02680/ECD_RS02685 | prophage tail fiber N‑terminal domain‑containing protein/hypothetical protein |
| ? | NC_012971 | = 1586961 | 0 (0.000) | pseudogene (2/1929 nt) | ECD_RS26210 | phage head spike fiber domain‑containing protein | |||||
| * | ? | NC_012971 | = 767939 | 0 (0.000) | 76 (1.130) +99 bp |
41/392 | 0.3 | 100% | intergenic (+22/+143) | ybcW/ECD_RS03870 | protein YbcW/YlcI/YnfO family protein |
| ? | NC_012971 | = 1427848 | NA (NA) | pseudogene (3/522 nt) | pdxI | pyridoxine 4‑dehydrogenase | |||||
| * | ? | NC_012971 | = 3365925 | NA (NA) | 102 (1.010) | 69/590 | 0.1 | 100% | pseudogene (474/480 nt) | ECD_RS16845 | aminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme |
| ? | NC_012971 | = 4153660 | 0 (0.000) | coding (132/1191 nt) | malE | maltose/maltodextrin ABC transporter substrate‑binding protein MalE | |||||
| * | ? | NC_012971 | = 3485246 | 116 (1.150) | 78 (1.220) | 50/374 | 0.1 | 68.0% | coding (3671/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_012971 | 3628983 = | 0 (0.000) | coding (411/873 nt) | ECD_RS18025 | polymorphic toxin type 34 domain‑containing protein | |||||
| * | ? | NC_012971 | 4159659 = | 0 (0.000) | 101 (1.000) | 56/590 | 0.4 | 100% | intergenic (+4/‑219) | ECD_RS20580/ubiC | SopA family protein/chorismate lyase |
| ? | NC_012971 | 4449936 = | NA (NA) | pseudogene (477/483 nt) | fimB | type 1 fimbria switch DNA invertase FimB | |||||
| * | ? | NC_012971 | = 4487090 | 0 (0.000) | 138 (1.400) | 73/574 | 0.1 | 100% | pseudogene (14/726 nt) | ECD_RS22230 | restriction endonuclease subunit S |
| ? | NC_012971 | 4487867 = | 0 (0.000) | intergenic (‑64/+69) | ECD_RS22235/ECD_RS22240 | IS1‑like element IS1A family transposase/restriction endonuclease subunit S | |||||