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 144,644 G→A P90L (CCC→CTC)  RPPX_00635 ← chemotaxis protein CheY
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 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 1,155,739 G→A P813P (CCG→CCA 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 1,157,314 A→C intergenic (+837/‑14446) RPPX_05120 → / → RPPX_05130 hypothetical protein/channel protein TolC
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_05775RPPX_05780 RPPX_05775, RPPX_05780
MC JC 1,343,208 Δ2,581 bp RPPX_05930RPPX_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
MC JC 1,508,761 Δ2,603 bp RPPX_06690RPPX_06695 RPPX_06690, RPPX_06695
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 1,561,742 G→C D410E (GAC→GAG RPPX_06985 ← DNA‑directed RNA polymerase subunit beta'
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 1,897,195 G→A intergenic (‑4973/‑3624) 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
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
RA 2,119,948 G→C intergenic (+8/‑9) RPPX_09485 → / → RPPX_09490 ATP synthase F0F1 subunit I/ATP synthase F0F1 subunit A
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_12300RPPX_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 3,148,563 G→A intergenic (+90/+122) RPPX_14035 → / ← RPPX_14040 membrane protein/bifunctional glyoxylate/hydroxypyruvate reductase B
JC 3,148,596 +96 bp intergenic (+123/+89) 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
JC JC 3,288,192 ISS12 (–) +7 bp :: +A intergenic (‑185/‑66) RPPX_14645 ← / → RPPX_14650 antibiotic transporter/TetR family transcriptional regulator
RA 3,297,192 Δ1 bp coding (157/921 nt) 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_15555RPPX_15560 RPPX_15555, RPPX_15560
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 4,147,332 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 4,165,118 Δ1 bp intergenic (‑312/‑163) 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
JC JC 4,401,667 ISS12 (–) +8 bp :: +A coding (261‑268/486 nt) RPPX_19665 ← GCN5 family acetyltransferase
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_21790RPPX_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
RA 5,598,979 C→T G235G (GGC→GGT RPPX_24920 → hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009974 341156–341386 342278 893–1123 162 [157] [159] 162 RPPX_01355/RPPX_01370 cytochrome C oxidase/cbb3‑type cytochrome c oxidase subunit I
* * ÷ CP009974 1155649 1155701 53 368 [45] [161] 162 RPPX_05115 hypothetical protein
* * ÷ CP009974 1155746 1155782 37 242 [0] [1] 320 RPPX_05115 hypothetical protein
* * ÷ CP009974 1156027 1156252 226 163 [160] [161] 169 RPPX_05120 hypothetical protein
* * ÷ CP009974 1156367 1156892 526 309 [27] [161] 164 [RPPX_05120] [RPPX_05120]
* * ÷ CP009974 1156907 1157206 300 173 [0] [0] 639 RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
* * ÷ CP009974 1157318 1158122–1157500 183–805 218 [0] [161] 163 RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
* * ÷ CP009974 5324682 5328654–5327261 2580–3973 288 [0] [160] 162 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 2596 =1 (0.000)213 (0.830) 143/284 0.8 99.8% intergenic (‑203/+211) RPPX_00010/RPPX_00015 integrase/peptidase S24
?CP009974 = 5798526 0 (0.000)intergenic (‑14/–) RPPX_25885/– integrase/–
* ? CP009974 418657 =0 (0.000)140 (0.720)
+AAGAAGC
92/214 1.9 97.7% intergenic (‑236/+415) RPPX_01715/RPPX_01720 hypothetical protein/lipoprotein
?CP009974 = 4147133 7 (0.030)intergenic (+385/‑636) RPPX_18425/RPPX_18430 enoyl‑CoA hydratase/conjugal transfer protein TraR
* ? CP009974 884033 =115 (0.420)185 (0.910)
+38 bp
119/224 0.4 68.2% intergenic (+81/+252) RPPX_03845/RPPX_03850 FAD‑binding protein/general secretion pathway protein GspN
?CP009974 = 884084 116 (0.430)intergenic (+132/+201) RPPX_03845/RPPX_03850 FAD‑binding protein/general secretion pathway protein GspN
* ? CP009974 1154348 =NA (NA)209 (1.020)
+37 bp
121/226 0.4 50.5% coding (1048/2580 nt) RPPX_05115 hypothetical protein
?CP009974 = 1155597 272 (1.000)coding (2297/2580 nt) RPPX_05115 hypothetical protein
* ? CP009974 1154854 =273 (1.000)185 (0.950)
+43 bp
111/214 0.6 65.5% coding (1554/2580 nt) RPPX_05115 hypothetical protein
?CP009974 1155783 = 1 (0.000)coding (2483/2580 nt) RPPX_05115 hypothetical protein
* ? CP009974 = 1155303505 (1.850)271 (1.060) 162/282 0.2 53.3% coding (2003/2580 nt) RPPX_05115 hypothetical protein
?CP009974 = 1156366 1 (0.000)coding (453/564 nt) RPPX_05120 hypothetical protein
* ? CP009974 = 115564845 (0.170)242 (1.440)
+57 bp
112/186 0.1 94.6% coding (2348/2580 nt) RPPX_05115 hypothetical protein
?CP009974 = 1155745 0 (0.000)coding (2445/2580 nt) RPPX_05115 hypothetical protein
* ? CP009974 1155977 =3 (0.010)314 (1.560)
+39 bp
122/222 0.3 74.4% coding (64/564 nt) RPPX_05120 hypothetical protein
?CP009974 = 1158685 290 (1.060)intergenic (+2208/‑13075) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
* ? CP009974 = 11569060 (0.000)173 (1.100)
+63 bp
85/174 0.9 67.2% intergenic (+429/‑14854) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
?CP009974 = 1160812 293 (1.080)intergenic (+4335/‑10948) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
* ? CP009974 1157207 =0 (0.000)255 (1.720) 72/164 1.6 100% intergenic (+730/‑14553) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
?CP009974 = 1158025 NA (NA)intergenic (+1548/‑13735) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
* ? CP009974 = 11573170 (0.000)165 (0.950)
+54 bp
74/192 2.9 65.3% intergenic (+840/‑14443) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
?CP009974 1160771 = 275 (1.010)intergenic (+4294/‑10989) RPPX_05120/RPPX_05130 hypothetical protein/channel protein TolC
* ? CP009974 1574780 =NA (NA)143 (0.790)
+50 bp
93/200 1.2 100% intergenic (‑136/+50) RPPX_07060/RPPX_07065 biotin‑‑protein ligase/5S ribosomal RNA
?CP009974 = 1915303 0 (0.000)intergenic (‑9/+117) RPPX_08540/RPPX_08545 5S ribosomal RNA/23S ribosomal RNA
* ? CP009974 = 16586120 (0.000)327 (1.240) 187/290 0.0 100% 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 1896077 =3053 (11.210)561 (2.310)
+CGCGAAAGTGGATGTC
108/268 2.7 28.0% intergenic (‑3855/‑4742) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
?CP009974 = 1898007 187 (0.690)intergenic (‑5785/‑2812) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
* ? CP009974 = 1897294NA (NA)1076 (4.090) 231/290 0.0 98.6% intergenic (‑5072/‑3525) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
?CP009974 1897952 = 16 (0.060)intergenic (‑5730/‑2867) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
* ? CP009974 1897301 =118 (0.430)859 (3.180)
+G
131/298 1.9 92.6% intergenic (‑5079/‑3518) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
?CP009974 1897958 = 20 (0.070)intergenic (‑5736/‑2861) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
* ? CP009974 1897973 =58 (0.210)794 (3.370) 178/260 0.0 94.0% 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 =164 (0.600)234 (1.280)
+49 bp
138/202 0.0 46.0% intergenic (‑6762/‑1835) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
?CP009974 = 1899234 654 (2.400)intergenic (‑7012/‑1585) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
* ? CP009974 1898984 =164 (0.600)400 (2.190)
+49 bp
157/202 0.0 59.3% intergenic (‑6762/‑1835) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
?CP009974 = 1899234 654 (2.400)intergenic (‑7012/‑1585) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
* ? CP009974 1898984 =164 (0.600)1165 (4.520)
+CGACTCGG
274/284 -0.0 83.9% intergenic (‑6762/‑1835) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
?CP009974 = 1899275 307 (1.130)intergenic (‑7053/‑1544) RPPX_08470/RPPX_08480 tryptophan synthase subunit beta/hypothetical protein
* ? CP009974 = 19015063 (0.010)339 (1.310) 171/286 0.1 99.6% coding (409/426 nt) RPPX_08485 hypothetical protein
?CP009974 1904110 = 0 (0.000)intergenic (+113/‑1737) RPPX_08495/RPPX_08505 ATPase AAA/hemolysin secretion protein D
* ? CP009974 2756352 =NA (NA)298 (1.090) 181/300 0.1 49.3% noncoding (2595/2595 nt) ISS12 repeat region
?CP009974 = 3238018 307 (1.130)coding (2588/2736 nt) secA preprotein translocase subunit SecA
* ? CP009974 = 3063941NA (NA)712 (2.780)
+TTTTTCCTG
234/282 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 = 3064036NA (NA)205 (0.760)
+TG
134/296 1.6 NA intergenic (+3/‑22) RPPX_13650/RPPX_13655 tRNA‑Ile/tRNA‑Ala
?CP009974 3064057 = NA (NA)intergenic (+24/‑1) RPPX_13650/RPPX_13655 tRNA‑Ile/tRNA‑Ala
* ? CP009974 3237442 =269 (0.990)354 (1.310) 199/298 0.0 57.0% coding (2012/2736 nt) secA preprotein translocase subunit SecA
?CP009974 3486774 = NA (NA)noncoding (1/2595 nt) ISS12 repeat region
* ? CP009974 = 35039154 (0.010)230 (0.900) 161/282 0.2 99.2% intergenic (‑249/+106) RPPX_15640/RPPX_15645 membrane protein/ATPase AAA
?CP009974 3506519 = 0 (0.000)intergenic (‑211/‑14) RPPX_15650/RPPX_15655 integrase/tRNA 2‑thiocytidine biosynthesis protein TtcA
* ? CP009974 = 3756397151 (0.550)237 (1.460)
+60 bp
117/180 0.0 71.1% intergenic (+279/+361) RPPX_16775/RPPX_16780 hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase
?CP009974 4031306 = 172 (0.630)intergenic (+448/‑336) RPPX_17905/RPPX_17915 23S rRNA methyltransferase/sulfurtransferase
* ? CP009974 = 3844204266 (0.980)95 (0.600)
+63 bp
67/174 2.8 38.2% intergenic (+1/‑42) RPPX_17125/RPPX_17130 tRNA‑Ala/tRNA‑Glu
?CP009974 3844237 = 266 (0.980)intergenic (+34/‑9) RPPX_17125/RPPX_17130 tRNA‑Ala/tRNA‑Glu
* ? CP009974 = 44257642 (0.010)229 (0.880) 152/288 0.5 99.6% intergenic (+687/‑204) RPPX_19805/RPPX_19815 hypothetical protein/integrase
?CP009974 4428367 = 0 (0.000)intergenic (+112/+608) RPPX_19820/RPPX_19830 ATPase AAA/ligand‑gated channel protein
* ? CP009974 = 53246810 (0.000)242 (0.930) 154/286 0.4 100% intergenic (+71/‑180) RPPX_23670/RPPX_23675 histidine kinase/integrase
?CP009974 5327261 = NA (NA)intergenic (+113/‑39) RPPX_23680/RPPX_23685 ATPase AAA/transposase