mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 52,146 | A→T | 2.7% | F95L (TTT→TTA) | rsmA ← | 16S rRNA m(6)A1518, m(6)A1519 dimethyltransferase, SAM‑dependent |
| RA | 233,731 | G→T | 3.1% | D75E (GAC→GAA) | mltD ← | putative membrane‑bound lytic murein transglycosylase D |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 308,537 | C→T | 3.3% | G266S (GGC→AGC) | ecpC ← | ECP production outer membrane protein |
| RA | 324,784 | A→G | 3.3% | L194P (CTG→CCG) | ykgH ← | putative inner membrane protein |
| JC | 545,679 | (TCA)4→3 | 3.2% | coding (683‑685/1050 nt) | allD ← | ureidoglycolate dehydrogenase |
| RA | 665,856 | A→G | 44.7% | L153P (CTG→CCG) | mrdB ← | cell wall shape‑determining protein |
| RA | 684,601 | G→A | 3.1% | P219S (CCG→TCG) | gltL ← | glutamate/aspartate ABC transporter ATPase |
| RA | 758,697 | G→T | 49.9% | intergenic (+292/‑9) | sdhB → / → sucA | succinate dehydrogenase, FeS subunit/2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| JC | 762,329 | Δ19 bp | 17.2% | coding (808‑826/1218 nt) | sucB → | dihydrolipoyltranssuccinase |
| RA | 935,501 | C→G | 4.2% | P760A (CCG→GCG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 963,530 | C→A | 3.0% | N512K (AAC→AAA) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,238,767 | T→C | 3.1% | S399S (TCT→TCC) | dadA → | D‑amino acid dehydrogenase |
| RA | 1,286,866 | A→G | 9.7% | intergenic (+340/+200) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,870 | C→A | 9.1% | intergenic (+344/+196) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,874 | G→A | 11.8% | intergenic (+348/+192) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,304,452 | Δ1 bp | 3.8% | coding (619/909 nt) | oppC → | oligopeptide ABC transporter permease |
| RA | 1,455,581 | T→C | 3.0% | W140R (TGG→CGG) | paaC → | ring 1,2‑phenylacetyl‑CoA epoxidase subunit |
| RA | 1,466,438 | T→G | 8.1% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,869,540 | G→A | 4.0% | A196T (GCC→ACC) | yeaH → | UPF0229 family protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,077,367 | C→T | 4.3% | H86Y (CAT→TAT) | cbeA → | CP4‑44 prophage, cytoskeleton bundling‑enhancing factor A, CbtA antitoxin |
| RA | 2,081,912 | G→T | 6.5% | I212I (ATC→ATA) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase, penicillin‑binding protein 6b |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,273,355 | T→C | 4.1% | F332L (TTT→CTT) | yejA → | microcin C ABC transporter periplasmic binding protein |
| RA | 2,308,405 | A→T | 3.9% | L70Q (CTG→CAG) | yojI ← | microcin J25 efflux ABC transporter permease/ATPase |
| RA | 2,327,132 | C→T | 3.4% | G342G (GGC→GGT) | atoB → | acetyl‑CoA acetyltransferase |
| RA | 2,478,543 | C→T | 5.1% | F233F (TTC→TTT) | dsdX → | D‑serine transporter |
| RA | 2,590,074 | G→A | 4.1% | E828K (GAA→AAA) | acrD → | aminoglycoside/multidrug efflux system |
| RA | 2,778,902 | Δ1 bp | 6.1% | coding (3823/4581 nt) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,817,907 | A→G | 5.4% | intergenic (‑49/+150) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,914 | T→G | 5.1% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,995 | A→G | 7.8% | intergenic (‑137/+62) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,032,961 | T→C | 4.7% | intergenic (+21/‑102) | yqfG → / → idi | uncharacterized protein/isopentenyl diphosphate isomerase |
| RA | 3,101,657 | C→T | 3.3% | intergenic (‑36/+148) | yggN ← / ← yggL | DUF2884 family putative periplasmic protein/DUF469 family protein |
| RA | 3,139,414 | T→C | 3.4% | F230F (TTT→TTC) | yghU → | putative S‑transferase |
| RA | 3,205,407 | A→G | 3.6% | M283T (ATG→ACG) | ttdR ← | transcriptional activator of ttdABT |
| RA | 3,372,182 | T→A | 11.4% | T131S (ACC→TCC) | nanT ← | sialic acid transporter |
| RA | 3,396,995 | A→G | 3.4% | F267L (TTC→CTC) | rng ← | ribonuclease G |
| RA | 3,688,286 | A→C | 12.7% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| RA | 3,747,144 | A→G | 3.2% | D21G (GAC→GGC) | lyxK → | L‑xylulose kinase |
| RA | 3,759,749 | T→A | 3.9% | I38F (ATC→TTC) | selB ← | selenocysteinyl‑tRNA‑specific translation factor |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,930,263 | A→G | 4.9% | L277P (CTC→CCC) | ravA ← | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| RA | 3,950,468 | T→G | 5.2% | intergenic (+49/‑38) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 3,973,264 | Δ1 bp | 4.2% | coding (744/1068 nt) | rffG → | dTDP‑glucose 4,6‑dehydratase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,006,702 | A→G | 3.3% | E280E (GAA→GAG) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,026,743 | A→G | 2.9% | Y73C (TAC→TGC) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,295,833 | T→C | 4.4% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 14.2% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 37.0% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 39.5% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583080 | 584689 | 1610 | 33 [32] | [31] 34 | [tfaX]–[ompT] | [tfaX], appY, [ompT] |
| * | * | ÷ | NC_000913 | 755130 | 758416 | 3287 | 34 [32] | [32] 34 | sdhC–sdhB | sdhC, sdhD, sdhA, sdhB |
| * | * | ÷ | NC_000913 | 2469044 | 2470750 | 1707 | 33 [32] | [31] 34 | [gtrB]–gtrS | [gtrB], gtrS |
| * | * | ÷ | NC_000913 | 2988724 | 2991672 | 2949 | 33 [32] | [32] 33 | [yqeI]–[ygeG] | [yqeI], yqeJ, yqeL, yqeK, ygeF, ygeF, [ygeG] |
| * | * | ÷ | NC_000913 | 3796807 | 3800534 | 3728 | 34 [32] | [32] 33 | [waaC]–[waaY] | [waaC], waaL, waaU, waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3804061 | 3805282 | 1222 | 33 [32] | [32] 33 | [waaB]–[waaP] | [waaB], waaS, [waaP] |
| * | * | ÷ | NC_000913 | 4541475 | 4541982 | 508 | 36 [32] | [32] 34 | [fimB] | [fimB] |
| * | * | ÷ | NC_000913 | 4542501 | 4542991 | 491 | 33 [31] | [31] 35 | [fimE] | [fimE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 80 (0.830) | 59/512 | NT | 98.8% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 315413 | 36 (0.370) | 3 (0.030) | 3/486 | NT | 8.1% | coding (123/300 nt) | insE1 | IS3 transposase A |
| ? | NC_000913 | = 315613 | NA (NA) | coding (27/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | NC_000913 | = 397900 | 108 (1.120) | 3 (0.030) | 3/500 | NT | 2.9% | coding (29/1095 nt) | yaiW | microcin Bac7 uptake protein, outer membrane surface‑exposed lipoprotein |
| ? | NC_000913 | = 398273 | 96 (1.020) | coding (402/1095 nt) | yaiW | microcin Bac7 uptake protein, outer membrane surface‑exposed lipoprotein | |||||
| * | ? | NC_000913 | = 689044 | NA (NA) | 4 (0.040) | 4/510 | NT | 8.9% | intergenic (‑31/+299) | insH1/lnt | IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase |
| ? | NC_000913 | = 754751 | 41 (0.430) | intergenic (‑283/‑426) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | NC_000913 | 1207790 = | 51 (0.530) | 40 (0.440) | 36/480 | NT | 50.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 30 (0.330) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 50 (0.520) | 35 (0.390) | 27/480 | NT | 47.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.330) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 76 (0.790) | 49/512 | NT | 98.7% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1738840 | 133 (1.380) | 3 (0.030) | 3/498 | NT | 2.8% | coding (997/1026 nt) | purR | transcriptional repressor, hypoxanthine‑binding |
| ? | NC_000913 | = 1739666 | 76 (0.810) | coding (133/933 nt) | ydhB | LysR family putative transcriptional regulator | |||||
| * | ? | NC_000913 | = 1879837 | 84 (0.870) | 3 (0.030) | 3/506 | NT | 3.5% | coding (112/360 nt) | yeaR | DUF1971 family protein, nitrate‑inducible |
| ? | NC_000913 | = 2515611 | NA (NA) | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 32 (0.330) | 25/512 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 66 (0.680) | 46/512 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 27 (0.280) | 26/512 | NT | 31.4% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 2876676 = | 59 (0.610) | coding (98/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | = 2290111 | NA (NA) | 37 (0.380) | 27/512 | NT | 38.9% | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 2876679 | 58 (0.600) | coding (101/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | = 2346516 | 107 (1.110) | 3 (0.030) | 3/508 | NT | 2.9% | coding (1654/2286 nt) | nrdA | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| ? | NC_000913 | = 2346713 | 95 (0.990) | coding (1851/2286 nt) | nrdA | ribonucleoside‑diphosphate reductase 1, alpha subunit | |||||
| * | ? | NC_000913 | = 3285841 | 86 (0.890) | 3 (0.030) | 3/506 | NT | 3.6% | coding (366/792 nt) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| ? | NC_000913 | = 3286053 | 77 (0.810) | coding (578/792 nt) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS | |||||
| * | ? | NC_000913 | = 3433347 | 110 (1.140) | 3 (0.030) | 3/500 | NT | 3.0% | coding (212/1125 nt) | smf | DNA recombination‑mediator A family protein |
| ? | NC_000913 | = 3433553 | 88 (0.930) | coding (6/1125 nt) | smf | DNA recombination‑mediator A family protein | |||||
| * | ? | NC_000913 | = 4094328 | 97 (1.010) | 3 (0.030) | 3/500 | NT | 2.8% | noncoding (14/402 nt) | REP299 (repetitive extragenic palindromic) element, contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element, contains 9 REP sequences |
| ? | NC_000913 | = 4094653 | 113 (1.200) | noncoding (339/402 nt) | REP299 (repetitive extragenic palindromic) element, contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element, contains 9 REP sequences | |||||
| * | ? | NC_000913 | = 4240749 | 103 (1.070) | 3 (0.030) | 3/492 | NT | 2.9% | intergenic (+15/+29) | psiE/xylE | phosphate starvation inducible protein/D‑xylose transporter |
| ? | NC_000913 | = 4240757 | 103 (1.110) | intergenic (+23/+21) | psiE/xylE | phosphate starvation inducible protein/D‑xylose transporter | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 7 (0.090) | 5/434 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4515803 = | 93 (0.960) | 3 (0.030) | 3/492 | NT | 3.0% | coding (876/2325 nt) | fecA | TonB‑dependent outer membrane ferric citrate transporter and signal transducer, ferric citrate extracelluar receptor, FecR‑interacting protein |
| ? | NC_000913 | 4516244 = | 104 (1.120) | coding (435/2325 nt) | fecA | TonB‑dependent outer membrane ferric citrate transporter and signal transducer, ferric citrate extracelluar receptor, FecR‑interacting protein | |||||
| * | ? | NC_000913 | 4544927 = | 70 (0.730) | 4 (0.040) | 4/498 | NT | 5.5% | coding (623/726 nt) | fimC | periplasmic chaperone |
| ? | NC_000913 | 4545204 = | 70 (0.750) | coding (108/2637 nt) | fimD | fimbrial usher outer membrane porin protein, FimCD chaperone‑usher | |||||