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 | annotation | gene | description |
| RA | 25,728 | G→A | intergenic (+153/‑418) | RPPX_00140 → / → RPPX_00145 | MarR family transcriptional regulator/(2Fe‑2S)‑binding protein |
| RA | 25,739 | A→T | intergenic (+164/‑407) | RPPX_00140 → / → RPPX_00145 | MarR family transcriptional regulator/(2Fe‑2S)‑binding protein |
| RA | 25,890 | G→A | intergenic (+315/‑256) | RPPX_00140 → / → RPPX_00145 | MarR family transcriptional regulator/(2Fe‑2S)‑binding protein |
| RA | 139,240 | G→T | intergenic (+242/+57) | RPPX_00595 → / ← RPPX_00600 | 3‑methylcrotonyl‑CoA carboxylase/Cro/Cl family transcriptional regulator |
| RA | 382,164 | T→C | intergenic (+300/+229) | RPPX_01535 → / ← RPPX_01540 | guanine permease/5‑hydroxyisourate hydrolase |
| RA | 382,181 | T→C | intergenic (+317/+212) | RPPX_01535 → / ← RPPX_01540 | guanine permease/5‑hydroxyisourate hydrolase |
| RA | 382,187 | C→T | intergenic (+323/+206) | RPPX_01535 → / ← RPPX_01540 | guanine permease/5‑hydroxyisourate hydrolase |
| RA | 382,193 | T→C | intergenic (+329/+200) | RPPX_01535 → / ← RPPX_01540 | guanine permease/5‑hydroxyisourate hydrolase |
| RA | 418,393 | C→T | C10Y (TGC→TAC) | RPPX_01715 ← | hypothetical protein |
| RA | 418,408 | C→G | C5S (TGC→TCC) | RPPX_01715 ← | hypothetical protein |
| RA | 418,441 | Δ1 bp | intergenic (‑20/+631) | RPPX_01715 ← / ← RPPX_01720 | hypothetical protein/lipoprotein |
| RA | 418,449 | Δ1 bp | intergenic (‑28/+623) | RPPX_01715 ← / ← RPPX_01720 | hypothetical protein/lipoprotein |
| RA | 542,045 | T→C | intergenic (‑306/+223) | argD ← / ← RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| RA | 542,069 | T→C | intergenic (‑330/+199) | argD ← / ← RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| RA | 542,073 | T→C | intergenic (‑334/+195) | argD ← / ← RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| RA | 542,098 | A→T | intergenic (‑359/+170) | argD ← / ← RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| RA | 542,104 | C→G | intergenic (‑365/+164) | argD ← / ← RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| RA | 542,115 | 2 bp→TG | intergenic (‑376/+152) | argD ← / ← RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| RA | 659,171 | A→G | V185A (GTC→GCC) | RPPX_02840 ← | ribonuclease D |
| RA | 753,050 | A→G | intergenic (+50/‑204) | RPPX_03275 → / → RPPX_03280 | porin/NAD‑dependent dehydratase |
| RA | 768,193 | A→G | G462G (GGT→GGC) | RPPX_03350 ← | acetolactate synthase |
| RA | 775,414 | C→T | intergenic (‑176/‑282) | RPPX_03375 ← / → RPPX_03380 | 16S ribosomal RNA/membrane protein |
| RA | 775,456 | G→A | intergenic (‑218/‑240) | RPPX_03375 ← / → RPPX_03380 | 16S ribosomal RNA/membrane protein |
| RA | 775,486 | G→A | intergenic (‑248/‑210) | RPPX_03375 ← / → RPPX_03380 | 16S ribosomal RNA/membrane protein |
| RA | 775,488 | G→C | intergenic (‑250/‑208) | RPPX_03375 ← / → RPPX_03380 | 16S ribosomal RNA/membrane protein |
| RA | 1,154,311 | T→C | T337T (ACT→ACC) | RPPX_05115 → | hypothetical protein |
| RA | 1,154,773 | 2 bp→GG | coding (1473‑1474/2580 nt) | RPPX_05115 → | hypothetical protein |
| RA | 1,155,980 | A→T | T23S (ACC→TCT) | RPPX_05120 → | hypothetical protein |
| RA | 1,155,982 | C→T | T23S (ACC→TCT) | RPPX_05120 → | hypothetical protein |
| RA | 1,158,307 | G→A | intergenic (+1830/‑13453) | RPPX_05120 → / → RPPX_05130 | hypothetical protein/channel protein TolC |
| RA | 1,158,399 | G→C | intergenic (+1922/‑13361) | RPPX_05120 → / → RPPX_05130 | hypothetical protein/channel protein TolC |
| RA | 1,158,403 | A→G | intergenic (+1926/‑13357) | RPPX_05120 → / → RPPX_05130 | hypothetical protein/channel protein TolC |
| RA | 1,159,719 | T→A | intergenic (+3242/‑12041) | RPPX_05120 → / → RPPX_05130 | hypothetical protein/channel protein TolC |
| RA | 1,174,412 | A→G | D407G (GAT→GGT) | RPPX_05135 → | ATP‑binding protein |
| RA | 1,247,078 | G→C | intergenic (‑212/‑599) | RPPX_05495 ← / → RPPX_05500 | glutamyl‑tRNA reductase/hypothetical protein |
| RA | 1,247,115 | 2 bp→T | intergenic (‑249/‑561) | RPPX_05495 ← / → RPPX_05500 | glutamyl‑tRNA reductase/hypothetical protein |
| MC JC | 1,303,424 | Δ2,602 bp | ISS12‑mediated | RPPX_05775–RPPX_05780 | RPPX_05775, RPPX_05780 |
| MC JC | 1,343,208 | Δ2,581 bp | RPPX_05930–RPPX_05935 | RPPX_05930, RPPX_05935 | |
| RA | 1,346,042 | 2 bp→GT | intergenic (+365/+561) | RPPX_05935 → / ← RPPX_05940 | ATPase AAA/DNA‑binding protein |
| RA | 1,358,374 | G→T | intergenic (+235/+2455) | RPPX_05970 → / ← RPPX_05980 | hypothetical protein/tRNA‑Thr |
| RA | 1,358,392 | C→A | intergenic (+253/+2437) | RPPX_05970 → / ← RPPX_05980 | hypothetical protein/tRNA‑Thr |
| RA | 1,358,394 | T→A | intergenic (+255/+2435) | RPPX_05970 → / ← RPPX_05980 | hypothetical protein/tRNA‑Thr |
| RA | 1,358,424 | 2 bp→TC | intergenic (+285/+2404) | RPPX_05970 → / ← RPPX_05980 | hypothetical protein/tRNA‑Thr |
| RA | 1,358,523 | C→A | intergenic (+384/+2306) | RPPX_05970 → / ← RPPX_05980 | hypothetical protein/tRNA‑Thr |
| RA | 1,449,631 | T→C | intergenic (+144/‑45) | RPPX_06395 → / → RPPX_06400 | chemotaxis protein/thiol:disulfide interchange protein |
| RA | 1,490,016 | G→A | intergenic (+31/‑317) | RPPX_06570 → / → RPPX_06575 | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/TonB‑dependent receptor |
| RA | 1,490,020 | G→C | intergenic (+35/‑313) | RPPX_06570 → / → RPPX_06575 | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/TonB‑dependent receptor |
| RA | 1,554,345 | A→T | V354V (GTT→GTA) | tuf ← | elongation factor Tu |
| RA | 1,554,630 | A→G | C259C (TGT→TGC) | tuf ← | elongation factor Tu |
| RA | 1,554,729 | C→A | G226G (GGG→GGT) | tuf ← | elongation factor Tu |
| RA | 1,554,744 | T→C | V221V (GTA→GTG) | tuf ← | elongation factor Tu |
| RA | 1,554,990 | A→G | D139D (GAT→GAC) | tuf ← | elongation factor Tu |
| RA | 1,555,277 | T→C | I44V (ATC→GTC) | tuf ← | elongation factor Tu |
| RA | 1,555,302 | A→G | V35V (GTT→GTC) | tuf ← | elongation factor Tu |
| RA | 1,796,148 | C→T | Y243Y (TAC→TAT) | RPPX_08005 → | integrase |
| RA | 1,896,148 | T→C | intergenic (‑3926/‑4671) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,896,150 | C→G | intergenic (‑3928/‑4669) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,896,637 | C→G | intergenic (‑4415/‑4182) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,027 | 4 bp→GACC | intergenic (‑4805/‑3789) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,132 | G→A | intergenic (‑4910/‑3687) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,594 | G→C | intergenic (‑5372/‑3225) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,654 | T→C | intergenic (‑5432/‑3165) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,666 | G→A | intergenic (‑5444/‑3153) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,669 | A→G | intergenic (‑5447/‑3150) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,916 | 2 bp→CT | intergenic (‑5694/‑2902) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,927 | A→G | intergenic (‑5705/‑2892) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| RA | 1,897,951 | G→T | intergenic (‑5729/‑2868) | RPPX_08470 ← / → RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| MC JC | 1,901,507 | Δ2,603 bp | [RPPX_08485]–RPPX_08495 | [RPPX_08485], RPPX_08490, RPPX_08495 | |
| RA | 1,915,165 | T→C | intergenic (+54/+14) | RPPX_08535 → / ← RPPX_08540 | ferrioxamine B receptor/5S ribosomal RNA |
| RA | 1,915,170 | Δ1 bp | intergenic (+59/+9) | RPPX_08535 → / ← RPPX_08540 | ferrioxamine B receptor/5S ribosomal RNA |
| RA | 1,915,172 | 3 bp→GTT | intergenic (+61/+5) | RPPX_08535 → / ← RPPX_08540 | ferrioxamine B receptor/5S ribosomal RNA |
| RA | 1,915,245 | A→G | noncoding (50/116 nt) | RPPX_08540 ← | 5S ribosomal RNA |
| RA | 1,920,735 | T→C | intergenic (‑364/+191) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,738 | T→C | intergenic (‑367/+188) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,747 | T→C | intergenic (‑376/+179) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,749 | A→C | intergenic (‑378/+177) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,754 | 1 bp→TTT | intergenic (‑383/+172) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,759 | C→T | intergenic (‑388/+167) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,761 | Δ1 bp | intergenic (‑390/+165) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,763 | A→C | intergenic (‑392/+163) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,765 | 2 bp→AC | intergenic (‑394/+160) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,768 | Δ1 bp | intergenic (‑397/+158) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,794 | G→T | intergenic (‑423/+132) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,920,803 | T→A | intergenic (‑432/+123) | RPPX_08560 ← / ← RPPX_08565 | 16S ribosomal RNA/CoA‑transferase |
| RA | 1,984,399 | T→C | intergenic (+229/+55) | RPPX_08865 → / ← RPPX_08870 | hypothetical protein/SulP family inorganic anion transporter |
| MC JC | 2,509,653 | Δ2,602 bp | RPPX_11210–[RPPX_11220] | RPPX_11210, RPPX_11215, [RPPX_11220] | |
| RA | 2,738,435 | C→T | Y216Y (TAC→TAT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,438 | C→T | H217H (CAC→CAT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,441 | A→T | V218V (GTA→GTT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,465 | T→C | A226A (GCT→GCC) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,471 | C→T | T228T (ACC→ACT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,498 | G→A | A237A (GCG→GCA) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,501 | T→C | G238G (GGT→GGC) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,507 | G→A | E240E (GAG→GAA) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,513 | G→A | K242K (AAG→AAA) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,522 | T→C | S245S (AGT→AGC) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,525 | T→C | A246A (GCT→GCC) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,529 | G→T | A248S (GCC→TCT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,531 | C→T | A248S (GCC→TCT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,537 | C→T | A250A (GCC→GCT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,546 | C→T | G253G (GGC→GGT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| RA | 2,738,549 | C→T | G254G (GGC→GGT) | RPPX_12165 → | benzene 1,2‑dioxygenase |
| MC JC | 2,747,118 | Δ2,603 bp | [RPPX_12205]–[RPPX_12220] | [RPPX_12205], RPPX_12210, RPPX_12215, [RPPX_12220] | |
| MC JC | 2,756,352 | Δ2,603 bp | [RPPX_12250]–RPPX_12260 | [RPPX_12250], RPPX_12255, RPPX_12260 | |
| MC JC | 2,767,372 | Δ2,604 bp | RPPX_12300–RPPX_12305 | RPPX_12300, RPPX_12305 | |
| JC | 2,783,938 | (CTTGCGTT)7→8 | intergenic (+386/‑55) | RPPX_12345 → / → RPPX_12350 | hypothetical protein/hypothetical protein |
| RA | 2,867,069 | G→A | intergenic (‑156/+60) | RPPX_12750 ← / ← RPPX_12755 | lipoyl synthase/DNA polymerase III subunit delta |
| RA | 2,910,161 | T→C | intergenic (+65/‑594) | gudD → / → RPPX_12965 | glucarate dehydratase/GABA permease |
| RA | 2,910,232 | T→C | intergenic (+136/‑523) | gudD → / → RPPX_12965 | glucarate dehydratase/GABA permease |
| RA | 2,910,258 | A→G | intergenic (+162/‑497) | gudD → / → RPPX_12965 | glucarate dehydratase/GABA permease |
| MC JC | 2,913,100 | Δ2,603 bp | RPPX_12970–[RPPX_12980] | RPPX_12970, RPPX_12975, [RPPX_12980] | |
| RA | 2,982,223 | T→G | intergenic (‑302/+644) | RPPX_13295 ← / ← RPPX_13300 | integrase/integrase |
| RA | 2,982,248 | T→G | intergenic (‑327/+619) | RPPX_13295 ← / ← RPPX_13300 | integrase/integrase |
| RA | 3,105,419 | G→A | intergenic (+140/+135) | RPPX_13820 → / ← mscL | ferredoxin‑NADP reductase/large‑conductance mechanosensitive channel |
| RA | 3,148,563 | G→A | intergenic (+90/+122) | RPPX_14035 → / ← RPPX_14040 | membrane protein/bifunctional glyoxylate/hydroxypyruvate reductase B |
| RA | 3,161,709 | T→C | intergenic (+115/+136) | RPPX_14090 → / ← RPPX_14095 | RND transporter/short‑chain dehydrogenase |
| RA | 3,297,192 | T→G | T53P (ACC→CCC) | RPPX_14685 ← | AraC family transcriptional regulator |
| RA | 3,400,410 | A→G | T381A (ACC→GCC) | RPPX_15160 → | chemotaxis protein |
| RA | 3,406,966 | +T | intergenic (+325/‑1049) | RPPX_15185 → / → RPPX_15195 | chemotaxis protein CheY/peptide chain release factor 2 |
| MC JC | 3,486,773 | Δ2,604 bp | RPPX_15555–RPPX_15560 | RPPX_15555, RPPX_15560 | |
| MC JC | 3,503,916 | Δ2,603 bp | RPPX_15645–RPPX_15650 | RPPX_15645, RPPX_15650 | |
| RA | 3,566,025 | T→G | intergenic (‑154/+160) | RPPX_15935 ← / ← RPPX_15940 | molecular chaperone/recombinase RdgC |
| RA | 3,566,031 | C→G | intergenic (‑160/+154) | RPPX_15935 ← / ← RPPX_15940 | molecular chaperone/recombinase RdgC |
| RA | 3,566,083 | C→T | intergenic (‑212/+102) | RPPX_15935 ← / ← RPPX_15940 | molecular chaperone/recombinase RdgC |
| RA | 3,585,070 | C→G | intergenic (+210/+13) | RPPX_16020 → / ← RPPX_16025 | hypothetical protein/diguanylate phosphodiesterase |
| RA | 3,673,509 | C→T | intergenic (+108/‑429) | RPPX_16400 → / → RPPX_16405 | glucose‑1‑phosphate thymidylyltransferase/beta‑ketoacyl synthase |
| RA | 3,721,374 | A→G | intergenic (+316/+51) | RPPX_16570 → / ← RPPX_16575 | glutathione S‑transferase/glutaredoxin |
| RA | 3,756,661 | T→C | intergenic (+543/+97) | RPPX_16775 → / ← RPPX_16780 | hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,756,668 | C→G | intergenic (+550/+90) | RPPX_16775 → / ← RPPX_16780 | hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,756,907 | G→C | L400V (CTC→GTC) | RPPX_16780 ← | phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,756,917 | G→A | T396T (ACC→ACT) | RPPX_16780 ← | phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,756,925 | G→C | Q394E (CAG→GAG) | RPPX_16780 ← | phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,756,930 | A→T | L392H (CTT→CAT) | RPPX_16780 ← | phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,756,936 | T→C | D390G (GAT→GGT) | RPPX_16780 ← | phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| RA | 3,793,987 | 2 bp→CC | coding (293‑294/3894 nt) | RPPX_16900 → | YD repeat‑/RHS repeat‑containing protein |
| RA | 3,837,678 | C→T | intergenic (+229/‑322) | RPPX_17095 → / → RPPX_17100 | proteophosphoglycan precursor/cupin |
| RA | 3,837,781 | C→T | intergenic (+332/‑219) | RPPX_17095 → / → RPPX_17100 | proteophosphoglycan precursor/cupin |
| RA | 3,837,790 | T→C | intergenic (+341/‑210) | RPPX_17095 → / → RPPX_17100 | proteophosphoglycan precursor/cupin |
| RA | 3,837,799 | A→G | intergenic (+350/‑201) | RPPX_17095 → / → RPPX_17100 | proteophosphoglycan precursor/cupin |
| RA | 3,844,127 | C→T | intergenic (+345/‑1) | RPPX_17120 → / → RPPX_17125 | glutamyl‑tRNA synthetase/tRNA‑Ala |
| JC | 3,858,455 | (GAAGCAA)5→13 | intergenic (+458/+161) | RPPX_17190 → / ← RPPX_17195 | aspartate‑semialdehyde dehydrogenase/hypothetical protein |
| JC | 3,898,294 | (TGGCCGTCGGGTTGCCGAGGACGGTGCAGACCGACTCAA)1→2 | coding (197/246 nt) | RPPX_17380 → | hypothetical protein |
| RA | 3,961,904 | C→T | T416T (ACC→ACT) | RPPX_17635 → | damage‑inducible protein CinA |
| RA | 3,971,951 | G→T | S9S (TCC→TCA) | RPPX_17675 ← | hemolysin D |
| RA | 4,030,927 | G→A | intergenic (+69/‑715) | RPPX_17905 → / → RPPX_17915 | 23S rRNA methyltransferase/sulfurtransferase |
| RA | 4,031,017 | Δ1 bp | intergenic (+159/‑625) | RPPX_17905 → / → RPPX_17915 | 23S rRNA methyltransferase/sulfurtransferase |
| RA | 4,132,231 | A→C | intergenic (+147/+82) | RPPX_18375 → / ← RPPX_18380 | membrane protein/phosphonoacetaldehyde hydrolase |
| RA | 4,147,169 | (CTTCTTG)5→6 | intergenic (+421/‑600) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,147,204 | A→G | intergenic (+456/‑565) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,147,209 | A→G | intergenic (+461/‑560) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,147,332 | A→T | intergenic (+584/‑437) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,147,342 | T→C | intergenic (+594/‑427) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,147,416 | C→G | intergenic (+668/‑353) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,147,431 | A→G | intergenic (+683/‑338) | RPPX_18425 → / → RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| RA | 4,165,100 | C→T | intergenic (‑294/‑181) | RPPX_18525 ← / → RPPX_18530 | transporter/16S ribosomal RNA |
| RA | 4,165,105 | G→A | intergenic (‑299/‑176) | RPPX_18525 ← / → RPPX_18530 | transporter/16S ribosomal RNA |
| RA | 4,165,107 | T→C | intergenic (‑301/‑174) | RPPX_18525 ← / → RPPX_18530 | transporter/16S ribosomal RNA |
| RA | 4,170,224 | T→C | noncoding (2917/2917 nt) | RPPX_18545 → | 23S ribosomal RNA |
| RA | 4,258,919 | C→G | intergenic (+132/+99) | prpE → / ← RPPX_18965 | propionyl‑CoA synthetase/ATPase |
| RA | 4,286,522 | C→T | intergenic (+378/+266) | RPPX_19070 → / ← RPPX_19075 | LacI family transcriptional regulator/hypothetical protein |
| RA | 4,363,550 | T→C | intergenic (+206/‑109) | RPPX_19410 → / → RPPX_19415 | alkyl hydroperoxide reductase/hypothetical protein |
| MC JC | 4,425,765 | Δ2,602 bp | RPPX_19815–RPPX_19820 | RPPX_19815, RPPX_19820 | |
| RA | 4,537,108 | A→G | Y105Y (TAT→TAC) | RPPX_20270 ← | hypothetical protein |
| RA | 4,537,135 | C→G | L96L (CTG→CTC) | RPPX_20270 ← | hypothetical protein |
| RA | 4,540,058 | T→C | A592A (GCA→GCG) | RPPX_20280 ← | hypothetical protein |
| RA | 4,540,457 | A→G | R459R (CGT→CGC) | RPPX_20280 ← | hypothetical protein |
| RA | 4,540,460 | C→T | R458R (CGG→CGA) | RPPX_20280 ← | hypothetical protein |
| RA | 4,541,504 | C→T | L110L (CTG→CTA) | RPPX_20280 ← | hypothetical protein |
| RA | 4,541,636 | C→T | P66P (CCG→CCA) | RPPX_20280 ← | hypothetical protein |
| RA | 4,541,648 | A→G | R62R (CGT→CGC) | RPPX_20280 ← | hypothetical protein |
| RA | 4,543,770 | A→G | A451A (GCT→GCC) | RPPX_20290 ← | hypothetical protein |
| RA | 4,543,776 | C→G | K449N (AAG→AAC) | RPPX_20290 ← | hypothetical protein |
| RA | 4,543,787 | G→A | L446L (CTA→TTA) | RPPX_20290 ← | hypothetical protein |
| RA | 4,543,809 | C→T | A438A (GCG→GCA) | RPPX_20290 ← | hypothetical protein |
| RA | 4,543,833 | C→G | S430S (TCG→TCC) | RPPX_20290 ← | hypothetical protein |
| RA | 4,544,682 | T→G | S147S (TCA→TCC) | RPPX_20290 ← | hypothetical protein |
| RA | 4,544,703 | G→A | P140P (CCC→CCT) | RPPX_20290 ← | hypothetical protein |
| RA | 4,544,907 | T→C | T72T (ACA→ACG) | RPPX_20290 ← | hypothetical protein |
| RA | 4,631,683 | G→A | intergenic (+245/‑585) | emrB → / → RPPX_20645 | multidrug resistance protein B/oxidoreductase |
| RA | 4,631,689 | Δ1 bp | intergenic (+251/‑579) | emrB → / → RPPX_20645 | multidrug resistance protein B/oxidoreductase |
| RA | 4,632,092 | C→G | intergenic (+654/‑176) | emrB → / → RPPX_20645 | multidrug resistance protein B/oxidoreductase |
| RA | 4,632,096 | G→C | intergenic (+658/‑172) | emrB → / → RPPX_20645 | multidrug resistance protein B/oxidoreductase |
| MC JC | 4,905,871 | Δ2,603 bp | RPPX_21790–RPPX_21795 | RPPX_21790, RPPX_21795 | |
| RA | 4,957,158 | C→G | V197V (GTC→GTG) | RPPX_21945 → | ATPase AAA |
| RA | 4,957,179 | C→T | D204D (GAC→GAT) | RPPX_21945 → | ATPase AAA |
| RA | 4,957,191 | G→A | A208A (GCG→GCA) | RPPX_21945 → | ATPase AAA |
| RA | 4,957,218 | C→T | D217D (GAC→GAT) | RPPX_21945 → | ATPase AAA |
| RA | 4,957,233 | 2 bp→GT | coding (666‑667/756 nt) | RPPX_21945 → | ATPase AAA |
| RA | 5,007,281 | A→T | Y68F (TAC→TTC) | RPPX_22185 → | phenylacetate‑‑CoA ligase |
| RA | 5,007,303 | T→C | D75D (GAT→GAC) | RPPX_22185 → | phenylacetate‑‑CoA ligase |
| RA | 5,007,323 | T→A | F82Y (TTC→TAC) | RPPX_22185 → | phenylacetate‑‑CoA ligase |
| RA | 5,007,375 | C→T | S99S (AGC→AGT) | RPPX_22185 → | phenylacetate‑‑CoA ligase |
| RA | 5,105,351 | T→C | P167P (CCA→CCG) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,354 | T→C | K166K (AAA→AAG) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,366 | A→G | N162N (AAT→AAC) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,372 | A→G | S160S (AGT→AGC) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,378 | A→G | F158F (TTT→TTC) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,383 | 2 bp→AA | coding (468‑469/1359 nt) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,402 | G→A | F150F (TTC→TTT) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,105,405 | T→A | R149R (CGA→CGT) | RPPX_22650 ← | benzene 1,2‑dioxygenase |
| RA | 5,157,352 | C→T | intergenic (+178/+65) | RPPX_22875 → / ← dnaE2 | integrase/DNA polymerase |
| MC JC | 5,273,059 | Δ2,603 bp | RPPX_23450–[RPPX_23460] | RPPX_23450, RPPX_23455, [RPPX_23460] | |
| RA | 5,305,850 | A→G | I115V (ATA→GTA) | RPPX_23590 → | leucyl‑tRNA synthetase |
| RA | 5,426,639 | T→C | V332V (GTA→GTG) | RPPX_24160 ← | damage‑inducible protein CinA |
| RA | 5,513,866 | G→A | A266V (GCA→GTA) | RPPX_24600 ← | integrase |
| RA | 5,513,872 | T→C | Q264R (CAG→CGG) | RPPX_24600 ← | integrase |
| RA | 5,515,235 | A→G | intergenic (‑22/+120) | RPPX_24605 ← / ← RPPX_24610 | transposase/hypothetical protein |
| RA | 5,595,953 | T→C | L225P (CTC→CCC) | RPPX_24915 → | hypothetical protein |
| RA | 5,597,121 | C→T | T614T (ACC→ACT) | RPPX_24915 → | hypothetical protein |
| RA | 5,597,130 | T→C | R617R (CGT→CGC) | RPPX_24915 → | hypothetical protein |
| MC MC JC | 5,798,527 | Δ2,603 bp | intergenic (‑15/–) | RPPX_25885 ← / – | integrase/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009974 | 341121–341386 | 342349 | 964–1229 | 259 [254] | [257] 260 | RPPX_01355/RPPX_01370 | cytochrome C oxidase/cbb3‑type cytochrome c oxidase subunit I |
| * | * | ÷ | CP009974 | 1155611 | 1155782 | 172 | 264 [250] | [7] 507 | RPPX_05115 | hypothetical protein |
| * | * | ÷ | CP009974 | 1156053 | 1156268 | 216 | 489 [18] | [257] 262 | RPPX_05120 | hypothetical protein |
| * | * | ÷ | CP009974 | 1156367 | 1156885 | 519 | 392 [29] | [254] 260 | [RPPX_05120] | [RPPX_05120] |
| * | * | ÷ | CP009974 | 1156907 | 1158136–1157500 | 594–1230 | 280 [0] | [256] 261 | RPPX_05120/RPPX_05130 | hypothetical protein/channel protein TolC |
| * | * | ÷ | CP009974 | 5324682 | 5328664–5327261 | 2580–3983 | 442 [0] | [252] 260 | RPPX_23675–RPPX_23690 | RPPX_23675,RPPX_23680,RPPX_23685,RPPX_23690 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009974 | 769996 = | NA (NA) | 169 (0.700) +50 bp |
107/200 | 2.1 | NA | intergenic (‑418/+50) | RPPX_03350/RPPX_03355 | acetolactate synthase/5S ribosomal RNA |
| ? | CP009974 | = 770170 | NA (NA) | intergenic (‑9/+117) | RPPX_03355/RPPX_03360 | 5S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | CP009974 | 884033 = | 160 (0.440) | 256 (0.940) +38 bp |
139/224 | 0.6 | 68.3% | intergenic (+81/+252) | RPPX_03845/RPPX_03850 | FAD‑binding protein/general secretion pathway protein GspN |
| ? | CP009974 | = 884084 | 159 (0.440) | intergenic (+132/+201) | RPPX_03845/RPPX_03850 | FAD‑binding protein/general secretion pathway protein GspN | |||||
| * | ? | CP009974 | 1154348 = | NA (NA) | 235 (0.930) +46 bp |
109/208 | 2.4 | 54.8% | coding (1048/2580 nt) | RPPX_05115 | hypothetical protein |
| ? | CP009974 | = 1155588 | 280 (0.770) | coding (2288/2580 nt) | RPPX_05115 | hypothetical protein | |||||
| * | ? | CP009974 | 1154348 = | NA (NA) | 271 (0.990) +37 bp |
123/226 | 2.0 | 58.2% | coding (1048/2580 nt) | RPPX_05115 | hypothetical protein |
| ? | CP009974 | = 1155597 | 259 (0.710) | coding (2297/2580 nt) | RPPX_05115 | hypothetical protein | |||||
| * | ? | CP009974 | 1154854 = | 340 (0.930) | 310 (1.200) +43 bp |
140/214 | 0.2 | 71.5% | coding (1554/2580 nt) | RPPX_05115 | hypothetical protein |
| ? | CP009974 | 1155783 = | 7 (0.020) | coding (2483/2580 nt) | RPPX_05115 | hypothetical protein | |||||
| * | ? | CP009974 | = 1155303 | 653 (1.800) | 351 (1.030) | 180/282 | 0.4 | 53.4% | coding (2003/2580 nt) | RPPX_05115 | hypothetical protein |
| ? | CP009974 | = 1156366 | 0 (0.000) | coding (453/564 nt) | RPPX_05120 | hypothetical protein | |||||
| * | ? | CP009974 | 1155488 = | 371 (1.020) | 416 (1.290) +AGGGTCCAGGGTGATGG |
137/266 | 3.0 | 71.6% | coding (2188/2580 nt) | RPPX_05115 | hypothetical protein |
| ? | CP009974 | = 1156052 | 1 (0.000) | coding (139/564 nt) | RPPX_05120 | hypothetical protein | |||||
| * | ? | CP009974 | 1155977 = | 1 (0.000) | 467 (1.740) +39 bp |
143/222 | 0.3 | 78.5% | coding (64/564 nt) | RPPX_05120 | hypothetical protein |
| ? | CP009974 | = 1158685 | 346 (0.950) | intergenic (+2208/‑13075) | RPPX_05120/RPPX_05130 | hypothetical protein/channel protein TolC | |||||
| * | ? | CP009974 | = 1156906 | 0 (0.000) | 274 (1.310) +63 bp |
89/174 | 2.6 | 73.5% | intergenic (+429/‑14854) | RPPX_05120/RPPX_05130 | hypothetical protein/channel protein TolC |
| ? | CP009974 | = 1160812 | 343 (0.940) | intergenic (+4335/‑10948) | RPPX_05120/RPPX_05130 | hypothetical protein/channel protein TolC | |||||
| * | ? | CP009974 | = 1508760 | 0 (0.000) | 292 (0.850) | 183/284 | 0.3 | 99.8% | intergenic (+932/‑204) | RPPX_06680/RPPX_06690 | membrane protein/integrase |
| ? | CP009974 | 1511364 = | 1 (0.000) | intergenic (+113/‑364) | RPPX_06695/RPPX_06700 | ATPase AAA/HxlR family transcriptional regulator | |||||
| * | ? | CP009974 | = 1658612 | 1 (0.000) | 277 (0.790) | 172/290 | 1.0 | 99.8% | intergenic (‑17/‑64) | RPPX_07420/RPPX_07425 | acyl‑CoA dehydrogenase/transposase |
| ? | CP009974 | 1659808 = | 0 (0.000) | intergenic (+152/+271) | RPPX_07425/RPPX_07430 | transposase/pyrroloquinoline quinone biosynthesis protein PqqE | |||||
| * | ? | CP009974 | = 1897294 | NA (NA) | 1099 (3.130) | 211/290 | 0.0 | 99.0% | intergenic (‑5072/‑3525) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | 1897952 = | 12 (0.030) | intergenic (‑5730/‑2867) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 1897973 = | 69 (0.190) | 839 (2.660) | 178/260 | 0.1 | 93.3% | intergenic (‑5751/‑2846) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | = 1898647 | NA (NA) | intergenic (‑6425/‑2172) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 1898984 = | 169 (0.460) | 281 (1.150) +49 bp |
135/202 | 0.2 | 47.9% | intergenic (‑6762/‑1835) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | = 1899234 | 741 (2.040) | intergenic (‑7012/‑1585) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 1898984 = | 169 (0.460) | 439 (1.800) +49 bp |
161/202 | 0.0 | 59.0% | intergenic (‑6762/‑1835) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | = 1899234 | 741 (2.040) | intergenic (‑7012/‑1585) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 1898984 = | 169 (0.460) | 1234 (3.580) +CGACTCGG |
275/284 | -0.0 | 84.4% | intergenic (‑6762/‑1835) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | = 1899275 | 313 (0.860) | intergenic (‑7053/‑1544) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | = 2649132 | 149 (0.410) | 317 (0.900) | 171/292 | 1.2 | 58.1% | intergenic (+274/+260) | RPPX_11785/putA | hypothetical protein/transcriptional regulator |
| ? | CP009974 | = 3847686 | 312 (0.880) | intergenic (+199/‑141) | RPPX_17150/RPPX_17155 | tRNA‑dihydrouridine synthase C/heat‑shock protein | |||||
| * | ? | CP009974 | = 3063941 | NA (NA) | 921 (2.690) +TTTTTCCTG |
252/282 | 0.0 | NA | intergenic (+52/‑16) | RPPX_13645/RPPX_13650 | 16S ribosomal RNA/tRNA‑Ile |
| ? | CP009974 | 3064156 = | NA (NA) | intergenic (+23/‑214) | RPPX_13655/RPPX_13660 | tRNA‑Ala/23S ribosomal RNA | |||||
| * | ? | CP009974 | = 3064033 | NA (NA) | 323 (0.920) +ATATG |
180/290 | 0.6 | NA | noncoding (77/77 nt) | RPPX_13650 | tRNA‑Ile |
| ? | CP009974 | 3064057 = | NA (NA) | intergenic (+24/‑1) | RPPX_13650/RPPX_13655 | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | CP009974 | = 3756397 | 253 (0.700) | 307 (1.410) +60 bp |
129/180 | 0.0 | 68.0% | intergenic (+279/+361) | RPPX_16775/RPPX_16780 | hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| ? | CP009974 | 4031306 = | 231 (0.640) | intergenic (+448/‑336) | RPPX_17905/RPPX_17915 | 23S rRNA methyltransferase/sulfurtransferase | |||||
| * | ? | CP009974 | = 5324681 | 0 (0.000) | 369 (1.060) | 195/286 | 0.1 | 100% | intergenic (+71/‑180) | RPPX_23670/RPPX_23675 | histidine kinase/integrase |
| ? | CP009974 | 5327261 = | NA (NA) | intergenic (+113/‑39) | RPPX_23680/RPPX_23685 | ATPase AAA/transposase | |||||