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 | seq id | position | mutation | annotation | gene | description |
| RA | AE015451_phaM1 | 144,577 | C→T | intergenic (+556/‑190) | PP_0136 CDS (conserved exported protein of unknown function) → / → gltP CDS (glutamate_aspartate‑proton DAACS transporter) | –/– |
| RA | AE015451_phaM1 | 278,744 | +A | intergenic (‑239/+75) | PP_0224 CDS (Monooxygenase_ DszC family) ← / ← sctC CDS (sulfur compound ABC transporter ‑ ATP‑binding subunit) | –/– |
| RA | AE015451_phaM1 | 307,866 | +C | intergenic (+881/‑988) | hslO CDS (33 kDa chaperonin) → / → PP_0254 CDS (conserved protein of unknown function) | –/– |
| RA | AE015451_phaM1 | 336,125 | +T | coding (210/237 nt) | PP_0278 CDS (conserved protein of unknown function) → | |
| RA | AE015451_phaM1 | 353,067 | A→G | intergenic (+34/+84) | hisF CDS (Imidazole glycerol phosphate synthase subunit HisF) → / ← cbcV CDS (choline _ betaine _ carnitine ABC transporter ‑ ATP binding subunit) | –/– |
| MC JC | AE015451_phaM1 | 386,865 | Δ1,248 bp | coding (5‑1252/1254 nt) | glyA‑I CDS (serine hydroxymethyltransferase) → | |
| RA | AE015451_phaM1 | 499,203 | A→G | intergenic (+47/‑249) | uhpA CDS (DNA‑binding response regulator UhpA) → / → PP_0411 CDS (Polyamine ABC transporter_ ATP‑binding protein) | –/– |
| RA | AE015451_phaM1 | 539,294 | A→C | T558P (ACC→CCC) | rpoB CDS (DNA‑directed RNA polymerase subunit beta) → | |
| RA | AE015451_phaM1 | 542,514 | C→G | L252V (CTG→GTG) | rpoC CDS (DNA‑directed RNA polymerase subunit beta') → | |
| MC JC | AE015451_phaM1 | 780,595 | Δ1,248 bp | coding (4‑1251/1254 nt) | glyA‑II CDS (serine hydroxymethyltransferase) ← | |
| RA | AE015451_phaM1 | 1,070,248 | +GA | intergenic (+48/+94) | aroP‑I CDS (aromatic amino acid transport protein) → / ← PP_0928 CDS (K+‑dependent Na+_Ca+ exchanger related‑protein) | –/– |
| MC JC | AE015451_phaM1 | 1,124,024 | Δ5,919 bp | [gcvT‑I CDS (aminomethyltransferase)]–[gcvH‑I CDS (glycine cleavage system H protein 1)] | [gcvT‑I CDS (aminomethyltransferase)], tdcG‑II CDS (L‑serine dehydratase), gcvP‑I CDS (glycine dehydrogenase), [gcvH‑I CDS (glycine cleavage system H protein 1)] | |
| RA | AE015451_phaM1 | 1,419,549 | +C | intergenic (‑38/+98) | PP_1242 CDS (conserved protein of unknown function) ← / ← PP_1244 CDS (conserved protein of unknown function) | –/– |
| RA | AE015451_phaM1 | 1,499,480 | 2 bp→AC | intergenic (+57/‑106) | trpS CDS (Tryptophan‑‑tRNA ligase) → / → zapE CDS (putative enzyme with nucleoside triphosphate hydrolase domain) | –/– |
| RA | AE015451_phaM1 | 1,499,498 | 1 bp→CG | intergenic (+75/‑89) | trpS CDS (Tryptophan‑‑tRNA ligase) → / → zapE CDS (putative enzyme with nucleoside triphosphate hydrolase domain) | –/– |
| RA | AE015451_phaM1 | 1,499,508 | +C | intergenic (+85/‑79) | trpS CDS (Tryptophan‑‑tRNA ligase) → / → zapE CDS (putative enzyme with nucleoside triphosphate hydrolase domain) | –/– |
| RA | AE015451_phaM1 | 1,713,060 | A→G | T2A (ACC→GCC) | tsaB CDS (endopeptidase) → | |
| MC JC | AE015451_phaM1 | 1,738,086 | Δ40,059 bp | [PP_1532 CDS (putative Phage integrase)]–[PP_1586 CDS (putative Killer protein)] | 60 genes [PP_1532 CDS (putative Phage integrase)], PP_1533 CDS (putative Excisionase), PP_1534 CDS (conserved protein of unknown function), PP_1535 CDS (putative Methyltransferase), PP_1536 CDS (conserved protein of unknown function), PP_1537 CDS (conserved protein of unknown function), PP_5472 CDS (conserved exported protein of unknown function), PP_1538 CDS (conserved protein of unknown function), PP_1539 CDS (conserved protein of unknown function), PP_1540 CDS (conserved protein of unknown function), PP_1541 CDS (putative Methyltransferase), PP_1542 CDS (conserved protein of unknown function), PP_1543 CDS (conserved protein of unknown function), PP_1544 CDS (conserved protein of unknown function), PP_1545 CDS (conserved protein of unknown function), PP_1546 CDS (conserved protein of unknown function), PP_5473 CDS (putative transcriptional regulator_ LuxR family), PP_5474 CDS (conserved protein of unknown function of phage origin), PP_1548 CDS (conserved protein of unknown function), PP_5744 CDS (conserved protein of unknown function_ phage origin), PP_1549 CDS (Transcriptional regulator_ Cro_CI family), PP_1550 CDS (Transcriptional regulator_ Cro_CI family), PP_1551 CDS (putative Phage replication protein O), PP_1552 CDS (putative Phage replication protein), PP_1553 CDS (conserved protein of unknown function), PP_1554 CDS (conserved protein of unknown function), PP_1555 CDS (putative Phage integrase), PP_1556 CDS (conserved protein of unknown function), PP_1557 CDS (conserved protein of unknown function), PP_1558 CDS (conserved protein of unknown function), PP_1559 CDS (Holin), PP_1560 CDS (conserved protein of unknown function), PP_1561 CDS (putative Phage holin), PP_1562 CDS (putative Phage terminase_ small subunit), PP_1563 CDS (putative Phage terminase_ large subunit), PP_1564 CDS (conserved exported protein of unknown function), PP_1565 CDS (Phage portal protein_ HK97 family), PP_1566 CDS (Peptidase U35), PP_1567 CDS (Capsid protein), PP_1568 CDS (conserved protein of unknown function), PP_1569 CDS (conserved protein of unknown function), PP_1570 CDS (Head‑tail adaptor), PP_1571 CDS (conserved protein of unknown function), PP_1572 CDS (conserved protein of unknown function), PP_1573 CDS (putative Major tail protein), PP_1574 CDS (conserved protein of unknown function), PP_1575 CDS (conserved protein of unknown function), PP_1576 CDS (putative Immunity protein), PP_1577 CDS (Phage tail tape meausure protein_ lambda family), PP_1578 CDS (conserved protein of unknown function), PP_5475 CDS (conserved protein of unknown function), PP_1579 CDS (conserved protein of unknown function), PP_1580 CDS (conserved protein of unknown function), PP_1581 CDS (BNR domain protein), PP_1582 CDS (conserved protein of unknown function), PP_1583 CDS (putative Structural protein P5), PP_1584 CDS (conserved protein of unknown function), PP_5476 CDS (conserved protein of unknown function), PP_1585 CDS (putative Antidote protein), [PP_1586 CDS (putative Killer protein)] |
|
| RA | AE015451_phaM1 | 1,932,640 | +C | intergenic (‑107/+43) | rluA CDS (23S rRNA (746) and tRNA (32) pseudouridine synthase) ← / ← minE CDS (Cell division topological specificity factor) | –/– |
| RA | AE015451_phaM1 | 2,586,629 | Δ1 bp | intergenic (+535/‑7) | PP_t39 tRNA (tRNA‑Leu) → / → PP_2266 CDS (DNA‑directed RNA polymerase_ bacteriophage and mitochondrial type) | –/– |
| MC JC | AE015451_phaM1 | 2,586,636 | Δ39,187 bp | [PP_2266 CDS (DNA‑directed RNA polymerase_ bacteriophage and mitochondrial type)]–[PP_2297 CDS (putative integrative genetic element Ppu40_ integrase)] | 42 genes [PP_2266 CDS (DNA‑directed RNA polymerase_ bacteriophage and mitochondrial type)], PP_5507 CDS (protein of unknown function), PP_2267 CDS (putative Phage single‑stranded DNA‑binding protein), PP_2268 CDS (Phage endodeoxyribonuclease I), PP_2269 CDS (putative N‑acetylmuramoyl‑L‑alanine amidase), PP_2270 CDS (putative DNA primase_helicase protein), PP_5508 CDS (conserved protein of unknown function), PP_5509 CDS (conserved exported protein of unknown function), PP_5510 CDS (protein of unknown function), PP_2272 CDS (conserved protein of unknown function), PP_5511 CDS (protein of unknown function), PP_2273 CDS (DNA polymerase I from phage origin), PP_2274 CDS (conserved protein of unknown function), PP_2275 CDS (conserved protein of unknown function), PP_2276 CDS (putative phage exonuclease), PP_2277 CDS (conserved protein of unknown function), PP_2278 CDS (conserved protein of unknown function), PP_5512 CDS (protein of unknown function), PP_2279 CDS (Head‑to‑tail joining protein), PP_2280 CDS (conserved protein of unknown function), PP_2281 CDS (putative Capsid assembly protein), PP_5513 CDS (conserved protein of unknown function of phage origin), PP_2282 CDS (Minor capsid protein 10), PP_2283 CDS (Tail tubular protein A), PP_2284 CDS (Tail tubular protein B), PP_5514 CDS (conserved protein of unknown function), PP_2285 CDS (conserved exported protein of unknown function), PP_2286 CDS (conserved protein of unknown function), PP_2287 CDS (Phage internal core protein), PP_2288 CDS (Phage tail fiber protein), PP_2289 CDS (conserved exported protein of unknown function), PP_2290 CDS (conserved protein of unknown function), PP_2291 CDS (conserved protein of unknown function), PP_2292 CDS (conserved protein of unknown function), PP_2293 CDS (DNA maturase B), PP_2294 CDS (conserved exported protein of unknown function), PP_5515 CDS (protein of unknown function), PP_5516 CDS (protein of unknown function), PP_5517 CDS (conserved exported protein of unknown function), PP_2295 CDS (putative antirestriction protein), PP_2296 CDS (conserved protein of unknown function), [PP_2297 CDS (putative integrative genetic element Ppu40_ integrase)] |
|
| MC JC | AE015451_phaM1 | 2,798,045 | Δ693 bp | coding (1‑693/693 nt) | endX CDS (extracellular DNA endonuclease) ← | |
| MC JC | AE015451_phaM1 | 3,366,695 | Δ15,777 bp | [PP_2964 CDS (putative transposase)]–[PP_2984 CDS (conserved protein of unknown function)] | 20 genes [PP_2964 CDS (putative transposase)], tnpC CDS (putative tnpA repressor TnpC), PP_2968 CDS (putative nickel_cobalt transporter_ high‑affinity), csoR CDS (putative repressor of copper utilisation proteins), PP_2970 CDS (conserved exported protein of unknown function), PP_2971 CDS (transposase), PP_2972 CDS (conserved protein of unknown function), dgkA‑II CDS (diacylglycerol kinase), PP_2974 CDS (putative sulfatase), PP_2975 CDS (Insertion element ISR1 uncharacterized 10 kDa protein A3), PP_2976 CDS (putative transposase), PP_mr38 ncRNA (ALIL regulatory region), tnpB CDS (Tn4652_ transposase subunit B), PP_2978 CDS (conserved protein of unknown function), PP_2979 CDS (conserved protein of unknown function), PP_2980 CDS (conserved protein of unknown function), tnpS CDS (putative cointegrate resolution protein S), tnpT‑I CDS (putative cointegrate resolution protein T Tn4652), PP_2983 CDS (conserved protein of unknown function), [PP_2984 CDS (conserved protein of unknown function)] |
|
| MC JC | AE015451_phaM1 | 3,412,992 | Δ35,612 bp | [PP_3026 CDS (putative Phage recombinase)]–PP_5557 CDS (protein of unknown function) | 47 genes [PP_3026 CDS (putative Phage recombinase)], PP_3027 CDS (conserved protein of unknown function), PP_3028 CDS (conserved protein of unknown function), PP_3029 CDS (DNA cytosine methyltransferase family protein), PP_3030 CDS (conserved exported protein of unknown function), prtN CDS (Transcription regulatory protein PrtN), PP_3032 CDS (DNA‑binding protein Roi‑related protein), PP_5552 CDS (conserved protein of unknown function), PP_5553 CDS (conserved protein of unknown function), PP_3033 CDS (putative transcriptional repressor_ CI_C2 family), PP_3034 CDS (putative Regulator protein), PP_3035 CDS (conserved protein of unknown function), PP_5554 CDS (protein of unknown function), PP_3036 CDS (conserved protein of unknown function), PP_5555 CDS (conserved protein of unknown function), PP_3037 CDS (C4‑type zinc finger protein_ DksA_TraR family), PP_3038 CDS (Pyocin R2_PP_ traC domain protein), PP_3039 CDS (conserved protein of unknown function), PP_3040 CDS (Pyocin R2_PP_ holin), PP_3041 CDS (conserved protein of unknown function), PP_3042 CDS (putative Terminase_ large subunit), PP_3043 CDS (conserved protein of unknown function), PP_3044 CDS (Phage portal protein_ lambda family), PP_3045 CDS (putative ClpP protease), PP_3046 CDS (conserved protein of unknown function), PP_3047 CDS (conserved protein of unknown function), PP_3048 CDS (conserved protein of unknown function), PP_3049 CDS (conserved protein of unknown function), PP_3050 CDS (conserved protein of unknown function), gpV CDS (Pyocin R2_PP_ tail spike protein), PP_3052 CDS (conserved protein of unknown function), gpW CDS (Pyocin R2_PP_ baseplate protein), gpJ CDS (Pyocin R2_PP_ baseplate_tail fiber protein), gpI CDS (Pyocin R2_PP_ tail formation protein), PP_3056 CDS (putative Pyocin R2_PP_ tail fiber protein), PP_3057 CDS (putative pectinesterase), PP_3058 CDS (conserved protein of unknown function), PP_3059 CDS (putative tail sheath protein), PP_3060 CDS (putative tail sheath protein), PP_3061 CDS (conserved protein of unknown function), PP_3062 CDS (putative Pyocin R2_PP_ tail length determination protein), gpU CDS (Pyocin R2_PP_ tail formation protein), PP_3064 CDS (Phage tail protein), gpD CDS (Pyocin R2_PP_ tail formation), PP_3066 CDS (Pyocin R2_PP_ lytic enzyme), PP_5556 CDS (putative bacteriophage lysis protein), PP_5557 CDS (protein of unknown function) |
|
| MC JC | AE015451_phaM1 | 3,760,510 | Δ22,673 bp | PP_3325 CDS (putative Outer membrane ferric siderophore receptor)–[nikD CDS (nickel ABC transporter ATP‑binding subunit)] | 22 genes PP_3325 CDS (putative Outer membrane ferric siderophore receptor), PP_3326 CDS (conserved exported protein of unknown function), PP_3328 CDS (putative Ring‑cleaving dioxygenase), PP_5599 CDS (putative transcriptional regulator_ LysR family), PP_3329 CDS (conserved membrane protein of unknown function), PP_5600 CDS (conserved protein of unknown function), PP_3330 CDS (putative Outer membrane ferric siderophore receptor), PP_3331 CDS (conserved membrane protein of unknown function), PP_3332 CDS (putative cytochrome c‑type protein), PP_3333 CDS (conserved protein of unknown function), PP_5743 CDS (putative TonB‑dependent receptor protein), PP_3335 CDS (conserved protein of unknown function), PP_3336 CDS (conserved protein of unknown function), PP_3337 CDS (conserved membrane protein of unknown function), PP_3338 CDS (putative cytochrome bd‑type quinol oxidase), PP_3339 CDS (conserved exported protein of unknown function), PP_3340 CDS (putative TonB‑dependent receptor), nikR CDS (nickel‑responsive regulator), nikA CDS (nickel ABC transporter periplasmic binding protein), nikB CDS (nickel ABC transporter permease subunit), nikC CDS (nickel ABC transporter permease subunit), [nikD CDS (nickel ABC transporter ATP‑binding subunit)] |
|
| MC JC | AE015451_phaM1 | 3,819,910 | Δ966 bp | coding (1‑966/966 nt) | endA CDS (endonuclease I) → | |
| RA | AE015451_phaM1 | 3,845,705 | +G | intergenic (‑72/+26) | PP_3394 CDS (putative 3‑hydroxy‑3‑methylglutaryl‑CoA lyase) ← / ← PP_3395 CDS (Transcriptional regulator_ LysR family) | –/– |
| RA | AE015451_phaM1 | 3,919,448 | G→C | A14P (GCC→CCC) | mobA CDS (Molybdenum cofactor guanylyltransferase) → | |
| RA | AE015451_phaM1 | 3,951,159 | T→C | intergenic (‑123/+72) | PP_3486 CDS (putative cytochrome c) ← / ← PP_3487 CDS (conserved exported protein of unknown function) | –/– |
| RA | AE015451_phaM1 | 3,951,161 | A→T | intergenic (‑125/+70) | PP_3486 CDS (putative cytochrome c) ← / ← PP_3487 CDS (conserved exported protein of unknown function) | –/– |
| MC JC | AE015451_phaM1 | 4,372,651 | Δ54,766 bp | PP_3849 CDS (putative calcium‑binding protein_ hemolysin‑type)–[PP_3920 CDS (putative Phage integrase)] | 78 genes PP_3849 CDS (putative calcium‑binding protein_ hemolysin‑type), PP_3850 CDS (conserved protein of unknown function), PP_5637 CDS (conserved protein of unknown function), PP_3851 CDS (conserved protein of unknown function), PP_3852 CDS (conserved protein of unknown function with BNR domain), PP_5638 CDS (conserved protein of unknown function), PP_3854 CDS (Lysozyme), PP_5639 CDS (conserved exported protein of unknown function), PP_3855 CDS (conserved protein of unknown function), PP_3856 CDS (conserved protein of unknown function), PP_3857 CDS (conserved protein of unknown function), PP_3858 CDS (putative Tail fiber protein), PP_3859 CDS (conserved protein of unknown function), PP_3860 CDS (Phage FluMu protein gp47), PP_3861 CDS (Phage FluMu protein gp46), PP_3862 CDS (putative Phage assembly protein), PP_3863 CDS (putative Phage tail protein), PP_3864 CDS (putative Phage FluMu DNA circulation protein), PP_3865 CDS (putative Phage tail protein), PP_5640 CDS (conserved protein of unknown function), PP_3866 CDS (conserved protein of unknown function), PP_3867 CDS (putative Phage tail tube protein), PP_3868 CDS (Group II intron‑encoding maturase), PP_3869 CDS (putative Phage sheath protein), PP_3870 CDS (Phage FluMu protein gp38), PP_3871 CDS (conserved protein of unknown function), PP_3873 CDS (conserved protein of unknown function), PP_3874 CDS (conserved protein of unknown function), PP_3875 CDS (conserved protein of unknown function), PP_3876 CDS (conserved protein of unknown function), PP_3877 CDS (conserved protein of unknown function), PP_3878 CDS (putative Phage minor capsid protein C), PP_3879 CDS (Phage portal protein_ HK97 family), PP_3880 CDS (conserved exported protein of unknown function), PP_3881 CDS (putative Phage terminase_ large subunit), PP_3882 CDS (putative Phage terminase_ small subunit), PP_3883 CDS (putative Phage holin), PP_3884 CDS (Phage holin_ lambda family), PP_5641 CDS (conserved protein of unknown function), PP_3886 CDS (conserved protein of unknown function), PP_3887 CDS (conserved protein of unknown function), PP_3888 CDS (conserved protein of unknown function), PP_3889 CDS (putative Phage integrase), PP_3890 CDS (conserved protein of unknown function), ybcO CDS (conserved protein of unknown function), PP_3892 CDS (conserved protein of unknown function), PP_3893 CDS (putative Phage DNA helicase), PP_3894 CDS (putative Phage replication protein O), PP_3895 CDS (putative Regulatory protein Cro), PP_3896 CDS (Transcriptional regulator_ Cro_CI family), PP_3897 CDS (conserved protein of unknown function), PP_3898 CDS (conserved protein of unknown function), PP_5643 CDS (conserved protein of unknown function), PP_5644 CDS (conserved membrane protein of unknown function), PP_3899 CDS (conserved protein of unknown function_ hicB family), PP_3900 CDS (hypothetical protein), PP_3901 CDS (conserved protein of unknown function), PP_3902 CDS (conserved protein of unknown function), PP_3903 CDS (conserved protein of unknown function), PP_3904 CDS (conserved protein of unknown function), PP_3905 CDS (Transcriptional regulator_ LuxR family), PP_3906 CDS (conserved protein of unknown function), PP_3907 CDS (conserved protein of unknown function), PP_3908 CDS (conserved protein of unknown function), PP_3909 CDS (conserved protein of unknown function), PP_3910 CDS (conserved protein of unknown function), PP_3911 CDS (conserved protein of unknown function), PP_3912 CDS (DNA‑cytosine methyltransferase), PP_3913 CDS (protein of unknown function), PP_5645 CDS (conserved protein of unknown function), PP_3914 CDS (conserved protein of unknown function), PP_5646 CDS (protein of unknown function), PP_3915 CDS (conserved protein of unknown function), PP_3916 CDS (conserved protein of unknown function), PP_5647 CDS (conserved protein of unknown function), PP_3917 CDS (conserved protein of unknown function), PP_3919 CDS (conserved protein of unknown function), [PP_3920 CDS (putative Phage integrase)] |
|
| RA | AE015451_phaM1 | 4,586,030 | 2 bp→TC | intergenic (+113/+101) | PP_4061 CDS (conserved protein of unknown function) → / ← PP_4063 CDS (putative Long‑chain‑fatty‑acid‑CoA ligase) | –/– |
| RA | AE015451_phaM1 | 4,586,035 | +G | intergenic (+118/+97) | PP_4061 CDS (conserved protein of unknown function) → / ← PP_4063 CDS (putative Long‑chain‑fatty‑acid‑CoA ligase) | –/– |
| RA | AE015451_phaM1 | 4,586,057 | +C | intergenic (+140/+75) | PP_4061 CDS (conserved protein of unknown function) → / ← PP_4063 CDS (putative Long‑chain‑fatty‑acid‑CoA ligase) | –/– |
| RA | AE015451_phaM1 | 4,740,811 | (T)7→6 | intergenic (+48/+705) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,740,816 | T→G | intergenic (+53/+700) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,740,819 | 2 bp→CT | intergenic (+56/+696) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,228 | +C | intergenic (+465/+288) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,230 | A→G | intergenic (+467/+286) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,232 | C→T | intergenic (+469/+284) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,235 | C→T | intergenic (+472/+281) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,238 | C→G | intergenic (+475/+278) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,240 | 2 bp→CT | intergenic (+477/+275) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,246 | Δ1 bp | intergenic (+483/+270) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,254 | +T | intergenic (+491/+262) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,258 | A→G | intergenic (+495/+258) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,262 | Δ1 bp | intergenic (+499/+254) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,263 | A→C | intergenic (+500/+253) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,272 | A→G | intergenic (+509/+244) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,274 | A→C | intergenic (+511/+242) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,276 | G→C | intergenic (+513/+240) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,278 | C→T | intergenic (+515/+238) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,283 | +T | intergenic (+520/+233) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,289 | C→G | intergenic (+526/+227) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,292 | C→T | intergenic (+529/+224) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,294 | C→G | intergenic (+531/+222) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,296 | A→C | intergenic (+533/+220) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| RA | AE015451_phaM1 | 4,741,298 | C→T | intergenic (+535/+218) | gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) | –/– |
| MC JC | AE015451_phaM1 | 4,919,155 | Δ69,176 bp | [PP_4328 CDS (conserved protein of unknown function)]–[ycgR CDS (Flagellar brake protein YcgR)] | 68 genes [PP_4328 CDS (conserved protein of unknown function)], [PP_4329 CDS (FlhB domain protein)], PP_4330 CDS (putative toxin‑related protein), PP_4331 CDS (conserved protein of unknown function), PP_4332 CDS (Chemotaxis protein CheW), PP_4333 CDS (CheW domain protein), PP_4334 CDS (ParA family protein), PP_4335 CDS (flagellar motor protein), PP_4336 CDS (flagellar motor rotation protein), cheBA CDS (chemotaxis response regulator protein‑glutamate methylesterase of group 1 operon), cheA CDS (Chemotaxis histidine kinase CheA), cheZ CDS (Protein phosphatase CheZ), cheY CDS (response regulator for chemotactic signal transduction), fliA CDS (RNA polymerase sigma 28 (sigma F) factor for class III flagellar operons), PP_4342 CDS (flagellar synthesis regulator_ putative ATPase), flhF CDS (Flagellar biosynthesis protein FlhF), flhA CDS (flagellar export pore protein), PP_4345 CDS (Transcriptional regulator_ GntR family), ddlA CDS (D‑alanine‑‑D‑alanine ligase A), PP_4348 CDS (putative Cystathionine beta‑lyase), PP_4349 CDS (conserved protein of unknown function), PP_4350 CDS (Aminotransferase_ class V_ NifS_IscS family), PP_5673 CDS (putative D‑alanine‑‑D‑alanine ligase), flhB CDS (flagellin export apparatus_ substrate specificity protein), fliR CDS (Flagellar biosynthetic protein fliR), fliQ CDS (flagellar export apparatus subunit), fliP CDS (flagellar export apparatus subunit), fliO CDS (Flagellar protein FliO), fliN CDS (C‑ring protein of the flagellar basal body), fliM CDS (flagellar synthesis_ switching and energizing component), fliL CDS (Flagellar protein FliL), fliK CDS (Flagellar hook‑length control protein FliK), PP_4362 CDS (conserved protein of unknown function), PP_4363 CDS (Sensor histidine kinase_response regulator), PP_4364 CDS (putative Anti‑sigma F factor antagonist), fliJ CDS (Flagellar protein FliJ), fliI CDS (flagellum‑specific ATP synthase), fliH CDS (Flagellar assembly protein FliH), fliG CDS (flagellar motor switch protein), fliF CDS (Flagellar M‑ring protein), fliE CDS (Flagellar hook‑basal body complex protein FliE), atoC CDS (two component system AtoC DNA‑binding transcriptional activator), fleS CDS (Sensory box histidine kinase FleS), fleQ CDS (Transcriptional regulator FleQ), fliT CDS (flagellar protein), fliS CDS (flagellar chaperone_ inhibits premature FliC assembly), fliD CDS (flagellar filament capping protein), PP_4377 CDS (putative Flagellin FlaG), fliC CDS (flagellin_ filament structural protein), PP_4379 CDS (Beta‑ketoacyl‑acyl‑carrier‑protein synthase I), flgL CDS (Flagellar hook‑associated protein FlgL), flgK CDS (Flagellar hook‑associated protein FlgK), flgJ CDS (Peptidoglycan hydrolase FlgJ), flgI CDS (Flagellar P‑ring protein), flgH CDS (Flagellar L‑ring protein), flgG CDS (flagellar basal‑body rod protein FlgG), flgF CDS (flagellar basal‑body rod protein FlgF), PP_4387 CDS (conserved exported protein of unknown function), flgE CDS (Flagellar hook protein FlgE), flgD CDS (Flagellar basal‑body rod modification protein FlgD), flgC CDS (flagellar basal‑body rod protein FlgC), flgB CDS (flagellar basal‑body rod protein FlgB), cheR CDS (chemotaxis protein methyltransferase), PP_4393 CDS (putative chemotaxis protein), flgA CDS (flagella basal body P‑ring formation protein), flgM CDS (Negative regulator of flagellin synthesis FlgM), PP_4396 CDS (conserved protein of unknown function), [ycgR CDS (Flagellar brake protein YcgR)] |
|
| MC JC | AE015451_phaM1 | 5,393,059 | Δ5,661 bp | [hsdR CDS (Type I restriction enzyme EcoAI R protein)]–[hsdS CDS (Type I restriction‑modification system_ S subunit)] | [hsdR CDS (Type I restriction enzyme EcoAI R protein)], hsdM CDS (Type I restriction enzyme EcoEI M protein), [hsdS CDS (Type I restriction‑modification system_ S subunit)] | |
| RA | AE015451_phaM1 | 5,555,608 | +GCC | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function) ← / ← PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| RA | AE015451_phaM1 | 5,659,798 | G→A | R281H (CGC→CAC) | metK CDS (methionine adenosyltransferase) → | |
| RA | AE015451_phaM1 | 5,674,751 | +G | intergenic (+113/+27) | rhlE‑II CDS (ATP‑dependent RNA helicase) → / ← yceI CDS (polyisoprene‑binding protein_ acidic stress response factor) | –/– |
| RA | AE015451_phaM1 | 5,674,753 | G→C | intergenic (+115/+25) | rhlE‑II CDS (ATP‑dependent RNA helicase) → / ← yceI CDS (polyisoprene‑binding protein_ acidic stress response factor) | –/– |
| RA | AE015451_phaM1 | 5,681,415 | +CGGG | intergenic (‑133/+71) | PP_4986 CDS (Channel protein_ hemolysin III family) ← / ← PP_4987 CDS (putative Chemotaxis protein) | –/– |
| RA | AE015451_phaM1 | 5,701,209 | C→A | intergenic (+1955/‑2050) | PP_5002 CDS (conserved protein of unknown function) → / → PP_5009 CDS (conserved protein of unknown function) | –/– |
| MC JC | AE015451_phaM1 | 5,918,836 | Δ4,582 bp | [gcvP‑II CDS (glycine dehydrogenase)]–[gcvT‑II CDS (aminomethyltransferase)] | [gcvP‑II CDS (glycine dehydrogenase)], gcvH‑II CDS (glycine cleavage system H protein 2), [gcvT‑II CDS (aminomethyltransferase)] | |
| RA | AE015451_phaM1 | 6,011,161 | T→C | intergenic (+90/+20) | xpt CDS (Xanthine phosphoribosyltransferase) → / ← PP_5266 CDS (putative acetyl‑CoA hydrolase family protein) | –/– |
| MC JC | AE015451_phaM1 | 6,159,202 | Δ6,596 bp | PP_5404 CDS (Transposition protein_ TnsC‑related protein)–PP_5407 CDS (Transposition protein_ TnsD‑related protein) | PP_5404 CDS (Transposition protein_ TnsC‑related protein), PP_5405 CDS (transposase), PP_5406 CDS (transposase), PP_5407 CDS (Transposition protein_ TnsD‑related protein) | |
| RA | pS4413_qbsFH | 87 | (CCGCG)1→2 | intergenic (–/‑1866) | – / → aadA CDS | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | AE015451_phaM1 | 2529185–2530862 | 2530883 | 22–1699 | 380 [338] | [0] 978 | PP_2218 CDS (transposase)–[PP_2219 CDS (conserved protein of unknown function)] | PP_2218 CDS (transposase),[PP_2219 CDS (conserved protein of unknown function)] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AE015451_phaM1 | = 1780066 | 257 (0.320) | 169 (0.230) | 69/256 | 2.7 | 44.4% | intergenic (+25/+81) | PP_1587 CDS (NhaP‑type Na+_H+ and K+_H+ antiporters)/dapC CDS (N‑succinyl‑L_L‑diaminopimelate aminotransferase alternative) | –/– |
| ? | AE015451_phaM1 | 1780129 = | 179 (0.240) | intergenic (+88/+18) | PP_1587 CDS (NhaP‑type Na+_H+ and K+_H+ antiporters)/dapC CDS (N‑succinyl‑L_L‑diaminopimelate aminotransferase alternative) | –/– | |||||
| * | ? | AE015451_phaM1 | 2301453 = | 0 (0.000) | 956 (1.240) | 112/264 | 0.4 | 100% | intergenic (‑97/‑234) | sbcD CDS (Exonuclease SbcD)/PP_5497 CDS (conserved protein of unknown function with rhs repeat‑associated core domain) | –/– |
| ? | AE015451_phaM1 | 2925429 = | NA (NA) | intergenic (‑177/+388) | PP_2563 CDS (putative Antibiotic biosynthesis protein)/PP_2564 CDS (putative Quercetin 2_3‑dioxygenase) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2301454 | 0 (0.000) | 816 (1.050) | 131/266 | 0.1 | 100% | intergenic (‑98/‑233) | sbcD CDS (Exonuclease SbcD)/PP_5497 CDS (conserved protein of unknown function with rhs repeat‑associated core domain) | –/– |
| ? | AE015451_phaM1 | 5545321 = | NA (NA) | intergenic (‑461/+416) | rpsF CDS (30S ribosomal protein S6)/rlmB CDS (23S rRNA (guanosine‑2'‑O‑)‑methyltransferase RlmB) | –/– | |||||
| * | ? | AE015451_phaM1 | = 2530859 | NA (NA) | 967 (1.250) | 111/264 | 0.4 | 100% | coding (98/369 nt) | PP_2219 CDS (conserved protein of unknown function) | |
| ? | AE015451_phaM1 | 2530884 = | 0 (0.000) | coding (123/369 nt) | PP_2219 CDS (conserved protein of unknown function) | ||||||
| * | ? | AE015451_phaM1 | 4496471 = | 28 (0.040) | 902 (1.140) | 125/270 | 0.2 | 97.0% | coding (781/960 nt) | PP_3987 CDS (Site‑specific recombinase_ phage integrase family) | |
| ? | AE015451_phaM1 | 4536203 = | NA (NA) | intergenic (+730/‑85) | PP_4022 CDS (conserved protein of unknown function)/PP_4024 CDS (transposase) | –/– | |||||
| * | ? | AE015451_phaM1 | = 4496478 | 83 (0.100) | 872 (1.100) | 137/270 | 0.1 | 91.3% | coding (788/960 nt) | PP_3987 CDS (Site‑specific recombinase_ phage integrase family) | |
| ? | AE015451_phaM1 | = 4538243 | NA (NA) | intergenic (+45/‑275) | PP_4025 CDS (transposase)/PP_4027 CDS (conserved protein of unknown function) | –/– | |||||
| * | ? | AE015451_phaM1 | = 5699642 | 678 (0.860) | 9721 (1.310) | 144/248 | 0.0 | 96.9% | intergenic (+388/‑3617) | PP_5002 CDS (conserved protein of unknown function)/PP_5009 CDS (conserved protein of unknown function) | –/– |
| ? | pS4413_qbsFH | 12 = | 0 (0.000) | intergenic (–/‑1941) | –/aadA CDS | –/– | |||||