breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 66,528 T→C Q8R (CAG→CGG)  araD ← L‑ribulose‑5‑phosphate 4‑epimerase
MC JC 66,533 3540 bp→27 bp [araD]araB [araD], araA, araB
RA 70,289 G→T intergenic (‑241/‑98) araB ← / → araC L‑ribulokinase/transcriptional regulator for ara operon
RA 78,003 A→C E128A (GAG→GCG)  yabM → putative transport protein
RA 283,759 T→G A445A (GCT→GCG yagF → putative dehydratase
MC JC 365,405 Δ93 bp coding (33‑125/3075 nt) lacZ ← beta‑D‑galactosidase
RA 502,653 C→T intergenic (‑191/+47) ybaL ← / ← fsr putative transport protein/fosmidomycin resistance protein
RA 547,694 A→G E38E (GAA→GAG b4507 → hypothetical protein
RA 547,835 +G coding (255/261 nt) b4507 → hypothetical protein
RA 704,236 T→C L357S (TTG→TCG)  nagE → PTS system, N‑acetylglucosamine‑specific enzyme IIABC
RA 1,056,041 A→G E186E (GAA→GAG torT → TorT
RA 1,302,782 A→G N2S (AAC→AGC)  oppD → OppD
RA 1,335,418 A→G S522G (AGC→GGC)  acnA → aconitate hydrase 1
RA 1,607,710 A→G L332P (CTT→CCT)  uxaB ← altronate oxidoreductase
RA 1,617,423 C→T R94C (CGC→TGC)  marR → MarR
RA 1,650,355 T→C F274L (TTC→CTC)  b1579 → putative transposase
RA 1,652,626 T→C E180E (GAA→GAG rspA ← starvation sensing protein
RA 1,718,191 A→G T98A (ACT→GCT)  slyB → putative outer membrane protein
RA 1,722,918 T→A N247Y (AAC→TAC)  b1647 ← hypothetical protein
RA 1,739,051 A→G M373V (ATG→GTG)  ydhC → putative transport protein
RA 1,741,574 2 bp→GA coding (94‑95/1374 nt) ydhE → putative transport protein
RA 1,812,482 T→C F198L (TTC→CTC)  katE → catalase
RA 1,860,370 T→C E28E (GAA→GAG yeaA ← hypothetical protein
RA 1,980,940 +C coding (1/363 nt)
coding (627/627 nt)
araH ←
araH ←
ABC‑type arabinose transport system permease component
ABC‑type arabinose transport system permease component
RA 2,008,480 +A coding (637/654 nt) yedK → hypothetical protein
RA 2,043,272 A→G S130G (AGT→GGT)  b1978 → hypothetical protein
RA 2,072,030 T→A C824S (TGC→AGC)  b2000 → outer membrane fluffing protein
RA 2,216,746 G→C S252S (TCC→TCG yehZ ← putative transport system permease protein
RA 2,429,483 T→C E65E (GAA→GAG dedD ← putative lipoprotein
RA 2,691,024 A→T F847Y (TTT→TAT)  purL ← phosphoribosylformyl‑glycineamide synthetase
RA 2,729,373 +C intergenic (‑195/+247) rrsG ← / ← clpB 16S ribosomal RNA/ClpB
RA 2,747,389 Δ1 bp coding (572/591 nt) b4540 → hypothetical protein
RA 2,751,091 G→C A426P (GCT→CCT)  recN → RecN
RA 2,766,382 C→G P218A (CCC→GCC)  b2632 → putative GTP‑binding protein
RA 2,766,423 G→A R231R (CGG→CGA b2632 → putative GTP‑binding protein
RA 2,766,427 2 bp→AC coding (697‑698/864 nt) b2632 → putative GTP‑binding protein
RA 2,766,473 A→G D248G (GAT→GGT)  b2632 → putative GTP‑binding protein
RA 2,766,475 A→G T249A (ACC→GCC)  b2632 → putative GTP‑binding protein
RA 2,781,020 +G intergenic (‑144/+65) ypjA ← / ← b2648 putative ATP‑binding component of a transport system/hypothetical protein
RA 2,781,027 C→G intergenic (‑151/+58) ypjA ← / ← b2648 putative ATP‑binding component of a transport system/hypothetical protein
RA 2,785,180 Δ1 bp coding (413/495 nt) b2655 → hypothetical protein
RA 2,806,762 T→C intergenic (+617/‑876) proX → / → b2682 high‑affinity transport system for glycine betaine and proline/hypothetical protein
RA 2,812,859 Δ1 bp intergenic (‑105/+46) ygaG ← / ← gshA hypothetical protein/gamma‑glutamate‑cysteine ligase
RA 2,820,144 Δ1 bp intergenic (+24/+18) b4542 → / ← oraA hypothetical protein/OraA
RA 2,823,915 A→G K21E (AAG→GAG)  srlA → PTS system, glucitol/sorbitol‑specific IIC component
RA 2,824,797 T→C F128S (TTT→TCT)  srlE → PTS system glucitol/sorbitol‑specific enzyme IIBC component
RA 2,825,102 T→C F230L (TTC→CTC)  srlE → PTS system glucitol/sorbitol‑specific enzyme IIBC component
RA 2,838,044 +G coding (498/1458 nt) ascF → PTS system enzyme IIBC
RA 2,838,055 Δ1 bp coding (509/1458 nt) ascF → PTS system enzyme IIBC
RA 2,842,033 G→T R67R (CGC→CGA hycG ← hydrogenase activity
RA 2,896,819 +C coding (622/657 nt) ygcU ← putative oxidoreductase subunit
RA 3,005,399 +C coding (1044/1092 nt) ygeW → putative carbamoyl transferase
RA 3,025,676 +C coding (535/570 nt) ygfQ → hypothetical protein
RA 3,075,220 (T)5→6 coding (256/357 nt) yggP ← hypothetical protein
RA 3,077,514 Δ1 bp intergenic (‑165/+149) cmtB ← / ← tktA PTS system mannitol‑specific enzyme IIA component/transketolase 1 isozyme
RA 3,077,640 +G intergenic (‑291/+23) cmtB ← / ← tktA PTS system mannitol‑specific enzyme IIA component/transketolase 1 isozyme
RA 3,077,905 A→G S584P (TCG→CCG)  tktA ← transketolase 1 isozyme
RA 3,078,245 C→G G470G (GGG→GGC tktA ← transketolase 1 isozyme
RA 3,099,661 (A)5→6 intergenic (‑19/+164) yggN ← / ← b2959 hypothetical protein/hypothetical protein
RA 3,107,469 +C intergenic (‑296/‑101) b2965 ← / → yqgA ornithine decarboxylase isozyme/putative transport protein
RA 3,108,438 C→A noncoding (56/76 nt) pheV → tRNA‑Phe
RA 3,115,116 +C coding (2013/2028 nt) b2974 ← putative endoglucanase
RA 3,123,585 +G coding (953/2286 nt) glcF ← glycolate oxidase iron‑sulfur subunit
RA 3,130,334 A→G V30V (GTT→GTC b2983 ← hypothetical protein
RA 3,152,247 +C intergenic (+10/+29) yghB → / ← yqhC hypothetical protein/putative ARAC‑type regulatory protein
JC 3,156,257 (CCA)2→1 coding (594‑596/930 nt) yqhG → hypothetical protein
RA 3,158,202 +C coding (961/975 nt) ygiRQ ← Fe‑S oxidoreductase
RA 3,166,935 2 bp→CG coding (312‑313/483 nt) b3023 ← hypothetical protein
RA 3,185,776 T→C F121L (TTC→CTC)  yqiG → putative membrane protein
RA 3,185,807 T→C F131S (TTT→TCT)  yqiG → putative membrane protein
RA 3,221,097 2 bp→GC coding (824‑825/3093 nt) b3076 → evolved beta‑D‑galactosidase alpha subunit
RA 3,222,944 4 bp→AGCA coding (2671‑2674/3093 nt) b3076 → evolved beta‑D‑galactosidase alpha subunit
RA 3,224,879 Δ1 bp coding (1005/1434 nt) ygjI → putative oxidoreductase
RA 3,224,926 +C coding (1052/1434 nt) ygjI → putative oxidoreductase
RA 3,236,177 Δ1 bp intergenic (+239/‑45) ygjR → / → ygjT hypothetical protein/putative transport protein
RA 3,236,735 +C coding (514/966 nt) ygjT → putative transport protein
RA 3,236,758 Δ1 bp coding (537/966 nt) ygjT → putative transport protein
RA 3,237,242 +C intergenic (+55/‑342) ygjT → / → ygjU putative transport protein/putative transport protein
RA 3,237,247 +C intergenic (+60/‑337) ygjT → / → ygjU putative transport protein/putative transport protein
RA 3,253,742 Δ1 bp coding (551/552 nt) yhaNM ← hypothetical protein
RA 3,255,594 Δ1 bp coding (4/1278 nt) yhaO ← putative transport system permease protein
RA 3,255,616 Δ1 bp intergenic (‑19/+312) yhaO ← / ← yhaP putative transport system permease protein/putative L‑serine dehydratase
RA 3,256,893 +C coding (405/423 nt) yhaQ ← putative L‑serine dehydratase
RA 3,257,838 +G coding (2222/2241 nt) tdcE ← putative formate acetyltransferase 3
RA 3,279,197 A→C R145S (AGA→AGC agaA → putative N‑acetylgalactosamine‑6‑phosphate deacetylase
RA 3,352,254 2 bp→GC intergenic (‑569/‑12) yhcC ← / → gltB hypothetical protein/glutamate synthase large subunit
RA 3,389,812 Δ1 bp intergenic (‑149/+4151) tldD ← / ← cafA TldD/CafA
RA 3,393,106 Δ1 bp intergenic (‑3443/+857) tldD ← / ← cafA TldD/CafA
RA 3,418,840 +G coding (1070/1089 nt) b3269 → putative transport system permease protein
RA 3,429,527 Δ1 bp coding (40/510 nt) yrdD ← putative DNA topoisomerase
RA 3,430,453 +C coding (745/747 nt) smf ← putative Rossmann‑fold nucleotide‑binding protein
RA 3,500,309 Δ1 bp coding (333/363 nt) b3372 → hypothetical protein
RA 3,509,958 Δ1 bp intergenic (‑195/+314) yhfZ ← / ← trpS hypothetical protein/tryptophan tRNA synthetase
RA 3,510,121 +G intergenic (‑358/+151) yhfZ ← / ← trpS hypothetical protein/tryptophan tRNA synthetase
RA 3,537,405 +GC intergenic (+61/‑394) b3407 → / → feoA hypothetical protein/ferrous iron transport protein A
RA 3,544,357 +G coding (163/1314 nt) gntT → gluconate permease
RA 3,544,360 +G coding (166/1314 nt) gntT → gluconate permease
RA 3,544,363 +C coding (169/1314 nt) gntT → gluconate permease
RA 3,548,005 C→T G701D (GGT→GAT)  malP ← maltodextrin phosphorylase
RA 3,554,088 +C coding (2/624 nt) yhgKJ ← RNA phosphage cyclase
RA 3,554,113 Δ1 bp coding (372/396 nt) yhgKJ ← RNA phosphage cyclase
RA 3,554,118 +C coding (367/396 nt) yhgKJ ← RNA phosphage cyclase
RA 3,558,932 2 bp→GC coding (153‑154/831 nt) glpG ← GlpG
RA 3,573,700 +C intergenic (+403/+997) yhgN → / ← gntK hypothetical protein/gluconokinase 2
RA 3,575,446 +G coding (912/942 nt) gntR ← GntR
RA 3,627,142 +G intergenic (‑24/+23) yhiH ← / ← yhiI putative ATP‑binding component of a transport system, fragment 1/putative membrane protein
RA 3,686,775 +T intergenic (‑23/+9) b3530 ← / ← yhjM putative oxidoreductase subunit/putative endoglucanase
RA 3,703,602 2 bp→GC intergenic (‑183/+124) dppB ← / ← dppA dipeptide transport system permease protein 1/dipeptide transport protein
RA 3,714,436 2 bp→GC coding (261‑262/660 nt) yiaD → putative outer membrane protein
RA 3,734,264 2 bp→GC coding (542‑543/825 nt) bax ← putative ATP‑binding protein
RA 3,737,956 2 bp→CG coding (623‑624/1254 nt) avtA → alanine‑alpha‑ketoisovalerate transaminase
RA 3,743,603 Δ1 bp coding (1171/1275 nt) yiaN → putative membrane protein
RA 3,754,310 C→A R382M (AGG→ATG)  yiaY ← putative oxidoreductase
JC 3,754,317 +GCG coding (1138/1149 nt) yiaY ← putative oxidoreductase
RA 3,765,234 G→A G129G (GGG→GGA yibJ → hypothetical protein
RA 3,870,631 Δ1 bp coding (610/1764 nt) dgoA ← 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA 3,870,765 +G coding (476/1764 nt) dgoA ← 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA 3,870,876 Δ1 bp coding (365/1764 nt) dgoA ← 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase
RA 3,872,450 +G coding (338/387 nt) yidW ← regulator protein for dgo operon
RA 3,873,627 Δ1 bp coding (506/672 nt) yidX → putative replicase
RA 3,876,595 G→C P385A (CCG→GCG)  gyrB ← DNA gyrase subunit B
RA 3,881,483 Δ1 bp intergenic (‑126/‑482) dnaA ← / → rpmH DnaA/50S ribosomal subunit protein L34
RA 3,896,324 +G coding (698/711 nt) b3718 ← putative isomerase
RA 3,927,062 +G coding (2/1284 nt)
coding (169/183 nt)
yieM ←
b4564 ←
hypothetical protein
hypothetical protein
RA 3,930,457 Δ1 bp coding (1515/1560 nt) kup → low affinity potassium transport system
RA 3,930,568 +G intergenic (+66/‑373) kup → / → rbsD low affinity potassium transport system/RbsD
RA 3,930,677 +G intergenic (+175/‑264) kup → / → rbsD low affinity potassium transport system/RbsD
JC 3,938,587 +TGC coding (220/546 nt) yiePs ← hypothetical protein
RA 3,941,734 Δ1 bp noncoding (409/2906 nt) rrlC → 23S ribosomal RNA
RA 3,944,676 2 bp→GC intergenic (+20/+75) trpT → / ← yifDA tRNA‑Trp/transcription regulator
RA 3,945,351 +C coding (1/600 nt)
coding (240/240 nt)
yifDA ←
yifDA ←
transcription regulator
transcription regulator
RA 3,950,557 2 bp→GC coding (451‑452/930 nt) ilvE → branched‑chain amino‑acid aminotransferase
RA 3,951,166 +C coding (35/1818 nt) ilvD → dihydroxyacid dehydratase
RA 3,951,168 +G coding (37/1818 nt) ilvD → dihydroxyacid dehydratase
RA 3,957,092 +CC intergenic (+26/+58) ilvC → / ← ppiC ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C
RA 3,957,124 +G intergenic (+58/+26) ilvC → / ← ppiC ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C
RA 3,957,548 1 bp→GG intergenic (‑117/‑744) ppiC ← / → rep peptidyl‑prolyl cis‑trans isomerase C/rep helicase
RA 3,957,551 +T intergenic (‑120/‑741) ppiC ← / → rep peptidyl‑prolyl cis‑trans isomerase C/rep helicase
RA 3,957,560 +C intergenic (‑129/‑732) ppiC ← / → rep peptidyl‑prolyl cis‑trans isomerase C/rep helicase
RA 3,958,877 2 bp→CG coding (586‑587/2022 nt) rep → rep helicase
RA 3,960,578 2 bp→CG coding (1266‑1267/1485 nt) gppA ← guanosine pentaphosphatase
RA 3,961,588 C→G R86T (AGG→ACG)  gppA ← guanosine pentaphosphatase
JC 3,968,317 +CGT coding (612/1170 nt) wecB → UDP‑N‑acetyl glucosamine ‑2‑epimerase
RA 3,969,103 2 bp→GC coding (232‑233/1263 nt) wecC → UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase
RA 3,971,075 2 bp→GC coding (942‑943/1068 nt) rffG → dTDP‑glucose 4,6‑dehydratase
RA 3,972,637 2 bp→GC coding (430‑431/546 nt) wecD → hypothetical protein
RA 3,975,313 Δ1 bp intergenic (+173/‑901) wzxE → / → wecF putative cytochrome/TDP‑Fuc4NAc:lipidII transferase
RA 3,978,702 C→T S68F (TCC→TTC)  yifK → putative amino acid/amine transport protein
RA 3,979,535 +G coding (1036/1386 nt) yifK → putative amino acid/amine transport protein
RA 3,979,546 Δ1 bp coding (1047/1386 nt) yifK → putative amino acid/amine transport protein
RA 3,980,918 2 bp→CG coding (348‑349/1236 nt) aslB → putative arylsulfatase regulator
RA 3,987,586 2 bp→GC coding (814‑815/963 nt) hemC ← porphobilinogen deaminase
RA 3,987,822 2 bp→CG coding (578‑579/963 nt) hemC ← porphobilinogen deaminase
RA 3,998,290 +G coding (379/486 nt) b4566 ← hypothetical protein
RA 4,001,421 2 bp→GC coding (381‑382/903 nt) rarD ← hypothetical protein
RA 4,001,486 2 bp→GC coding (316‑317/903 nt) rarD ← hypothetical protein
RA 4,001,717 +C coding (86/903 nt) rarD ← hypothetical protein
RA 4,004,979 +G coding (1511/1833 nt) recQ → ATP‑dependent DNA helicase
RA 4,004,984 +CG coding (1516/1833 nt) recQ → ATP‑dependent DNA helicase
RA 4,005,601 +C coding (237/282 nt) b4568 → hypothetical protein
RA 4,006,483 +C coding (183/207 nt) b4554 ← hypothetical protein
RA 4,007,718 2 bp→CG coding (943‑944/1023 nt) pldB → lysophospholipase L(2)
RA 4,007,907 +GG intergenic (+109/‑11) pldB → / → b4555 lysophospholipase L(2)/hypothetical protein
RA 4,008,375 +A coding (458/516 nt) b4555 → hypothetical protein
RA 4,008,391 +C coding (474/516 nt) b4555 → hypothetical protein
RA 4,008,393 C→G A159G (GCT→GGT)  b4555 → hypothetical protein
RA 4,008,421 +T coding (504/516 nt) b4555 → hypothetical protein
RA 4,008,429 +TG coding (512/516 nt) b4555 → hypothetical protein
RA 4,008,469 +G intergenic (+36/‑197) b4555 → / → yigM hypothetical protein/hypothetical protein
RA 4,008,473 +G intergenic (+40/‑193) b4555 → / → yigM hypothetical protein/hypothetical protein
RA 4,008,491 2 bp→CG intergenic (+58/‑174) b4555 → / → yigM hypothetical protein/hypothetical protein
RA 4,008,525 +G intergenic (+92/‑141) b4555 → / → yigM hypothetical protein/hypothetical protein
RA 4,013,176 C→G G182R (GGA→CGA)  ysgA ← hypothetical protein
RA 4,013,177 +C coding (543/999 nt) ysgA ← hypothetical protein
RA 4,013,717 +G coding (3/999 nt) ysgA ← hypothetical protein
RA 4,013,772 +C intergenic (‑53/‑246) ysgA ← / → udp hypothetical protein/uridine phosphorylase
RA 4,016,743 C→T P101L (CCC→CTC)  ubiE → UbiE
RA 4,019,857 C→T intergenic (+56/‑28) b3836 → / → b3838 hypothetical protein/hypothetical protein
RA 4,019,860 Δ2 bp intergenic (+59/‑24) b3836 → / → b3838 hypothetical protein/hypothetical protein
RA 4,021,684 Δ1 bp coding (542/609 nt)|coding (1/243 nt) b4556 →
tatD →
hypothetical protein
Mg‑dependent DNase
RA 4,026,252 2 bp→GC coding (110‑111/1164 nt) fadA ← thiolase I
RA 4,031,984 +C coding (1250/1299 nt) trkH → TrkH
RA 4,039,960 Δ1 bp intergenic (+42/‑36) yihD → / → yihE hypothetical protein/hypothetical protein
RA 4,041,654 G→A intergenic (+29/‑125) dsbA → / → b3861 protein disulfide isomerase I/putative GTP‑binding protein
RA 4,041,671 (T)6→7 intergenic (+46/‑108) dsbA → / → b3861 protein disulfide isomerase I/putative GTP‑binding protein
RA 4,051,144 Δ1 bp intergenic (+146/+305) hemN → / ← glnG O2‑independent coproporphyrinogen III oxidase/GlnG
RA 4,051,170 +C intergenic (+172/+279) hemN → / ← glnG O2‑independent coproporphyrinogen III oxidase/GlnG
RA 4,057,759 +C coding (1773/1776 nt) yihK → putative GTP‑binding factor
RA 4,061,961 Δ1 bp coding (1386/1458 nt) b3876 ← putative permease
RA 4,085,675 Δ1 bp intergenic (+38/+13) yiiG → / ← frvR hypothetical protein/putative frv operon regulatory protein
RA 4,091,351 C→T G168D (GGC→GAC)  rhaD ← rhamnulose‑phosphate aldolase
MC JC 4,091,572 3461 bp→29 bp [rhaD]rhaB [rhaD], rhaA, rhaB
RA 4,103,519 +T intergenic (‑268/‑530) cpxR ← / → yiiP transcriptional regulator in 2‑component system/putative transport system permease protein
RA 4,139,669 +C coding (233/330 nt)
coding (132/159 nt)
yijI →
b4558 ←
hypothetical protein
hypothetical protein
RA 4,158,827 G→T G61V (GGC→GTC)  yijC → hypothetical protein
RA 4,161,702 C→G A162G (GCA→GGA)  btuB → BtuB
RA 4,175,949 +G intergenic (+82/‑76) nusG → / → rplK NusG/50S ribosomal subunit protein L11
RA 4,194,577 2 bp→GC coding (97‑98/774 nt) yjaD → hypothetical protein
RA 4,293,960 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate‑aspartate symport protein/hypothetical protein
RA 4,311,496 +C coding (301/408 nt) phnQ ← hypothetical protein
RA 4,316,203 T→A Q47L (CAG→CTG)  phnK ← ATP‑binding component of phosphonate transport
RA 4,435,684 +A coding (400/501 nt) ytfI → hypothetical protein
RA 4,448,541 +C intergenic (+46/‑92) ytfQ → / → ytfR putative LACI‑type transcriptional regulator/YtfR
RA 4,448,543 +C intergenic (+48/‑90) ytfQ → / → ytfR putative LACI‑type transcriptional regulator/YtfR
RA 4,449,738 +G coding (1106/1254 nt) ytfR → YtfR
RA 4,472,408 A→G intergenic (+117/‑28) b4251 → / → b4252 hypothetical protein/hypothetical protein
RA 4,474,826 +A intergenic (+1/+44) yjgL → / ← argI hypothetical protein/ornithine carbamoyltransferase 1
MC JC 4,474,849 20 bp→30 bp intergenic (+24/+2) yjgL → / ← argI hypothetical protein/ornithine carbamoyltransferase 1
RA 4,477,041 Δ1 bp intergenic (‑151/‑269) b4256 ← / → yjgN hypothetical protein/hypothetical protein
RA 4,477,068 +C intergenic (‑178/‑242) b4256 ← / → yjgN hypothetical protein/hypothetical protein
RA 4,477,281 Δ1 bp intergenic (‑391/‑29) b4256 ← / → yjgN hypothetical protein/hypothetical protein
RA 4,477,321 Δ1 bp coding (12/1182 nt) yjgN → hypothetical protein
RA 4,478,503 (A)7→6 intergenic (+12/+47) yjgN → / ← valS hypothetical protein/valine tRNA synthetase
RA 4,478,511 Δ1 bp intergenic (+20/+39) yjgN → / ← valS hypothetical protein/valine tRNA synthetase
RA 4,478,527 Δ1 bp intergenic (+36/+23) yjgN → / ← valS hypothetical protein/valine tRNA synthetase
RA 4,501,186 (T)6→7 intergenic (‑187/‑440) yi41 ← / → b4279 IS4 hypothetical protein/putative transport protein
RA 4,542,643 Δ1 bp intergenic (+46/‑22) b4316 → / → fimD Pil/FimD
RA 4,544,170 T→C I502I (ATT→ATC fimD → FimD
RA 4,573,190 Δ1 bp coding (1487/1542 nt) yjiU → hypothetical protein
RA 4,583,050 G→A Q446* (CAA→TAA)  hsdR ← endonuclease R
RA 4,593,254 2 bp→GC coding (59‑60/807 nt) yjjM ← hypothetical protein
RA 4,593,336 +G intergenic (‑23/‑208) yjjM ← / → yjjN hypothetical protein/putative oxidoreductase
RA 4,600,078 C→T W135* (TGG→TAG)  yjjP ← putative structural protein
RA 4,608,595 2 bp→GC intergenic (+23/‑369) prfC → / → osmY peptide chain release factor RF‑3/OsmY
RA 4,614,238 G→T L133I (CTA→ATA)  yjjI ← hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 950479 952811 2333 62 [60] [60] 62 pflB pflB
* * ÷ NC_000913 1294640 1297386 2747 62 [60] [61] 62 adhE adhE
* * ÷ NC_000913 1396764 1440913 44150 63 [60] [59] 62 fnr–ldhA fnr,ogt,ydaH,b1337,ydaJ,ydaK,ydaL,b1341,b1342,dbpA,ydaO,b1345,ydaQ,ydaC,lar,recT,recE,racC,ydaE,ydaD,sieB,ydaF,b1355,ydaR,ydaS,ydaT,ydaU,b1360,ydaW,b1362,trkG,b1364,b1365,ydaY,b1367,b1368,b1369,trs55,b1371,b1372,ynaC,b1374,ynaE,ynaF,b1377,ydbK,hslJ,ldhA
* * ÷ NC_000913 1976519 1977294–1976527 9–776 110 [0] [0] 87 insB5–insA5 insB5,insA5
* * ÷ NC_000913 2412711 2414931 2221 66 [61] [61] 63 pta pta
* * ÷ NC_000913 2518989–2519026 2519130–2519066 41–142 66 [61] [61] 62 [valU]–[valX] [valU],[valX]
* * ÷ NC_000913 3943583–3943706 3943797–3943771 66–215 68 [60] [61] 63 rrlC 23S ribosomal RNA
* * ÷ NC_000913 4376912 4378123 1212 62 [60] [61] 62 [frdD]–[frdA] [frdD],frdC,frdB,[frdA]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 244129 =174 (1.090)160 (1.160)
+ACTTCGCCCA
50/130 1.9 51.7% intergenic (+8/‑198) gmhA/yafJ phosphoheptose isomerase/putative amidotransferase
?NC_000913 757626 = 172 (1.080)coding (715/717 nt) sdhB succinate dehydrogenase iron sulfur protein
* ? NC_000913 269765 =NA (NA)132 (0.830) 81/150 0.5 29.8% coding (300/405 nt) yi91a hypothetical protein
?NC_000913 = 370983 311 (1.960)coding (536/882 nt) mhpC 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
* ? NC_000913 = 279335NA (NA)135 (0.850) 78/150 0.6 30.0% coding (252/339 nt) b4505 hypothetical protein
?NC_000913 370982 = 315 (1.980)coding (535/882 nt) mhpC 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
* ? NC_000913 1207013 =39 (0.250)86 (0.690) 64/118 0.5 74.9% coding (290/630 nt) ycfK hypothetical protein
?NC_000913 1208842 = 27 (0.220)coding (40/540 nt) b1157 putative tail fiber protein
* ? NC_000913 = 120702838 (0.240)83 (0.670) 54/118 1.1 74.5% coding (305/630 nt) ycfK hypothetical protein
?NC_000913 = 1208825 27 (0.220)coding (57/540 nt) b1157 putative tail fiber protein
* ? NC_000913 = 1395262NA (NA)109 (0.690) 71/150 1.0 100% intergenic (+146/‑127) trs54/ynaJ IS5 transposase/hypothetical protein
?NC_000913 = 1976518 0 (0.000)intergenic (‑297/+24) b1892/insB5 FlhD/IS1 protein InsB
* ? NC_000913 1977295 =0 (0.000)85 (0.530) 60/150 1.8 100% intergenic (‑56/‑482) insA5/yecG IS1 protein InsA/putative regulator
?NC_000913 = 2100969 NA (NA)coding (443/474 nt)
coding (443/444 nt)
b4529
yefJ
hypothetical protein
putative glycosyl transferase
* ? NC_000913 3192559 =134 (0.840)65 (0.550)
+ATGTGTTAATGAAACCTTC
42/112 2.0 40.0% intergenic (+18/+402) b3051/b3052 putative membrane protein/putative kinase
?NC_000913 = 3192916 128 (0.810)intergenic (+375/+45) b3051/b3052 putative membrane protein/putative kinase
* ? NC_000913 3349258 =18 (0.110)117 (0.740) 70/150 1.0 86.7% coding (1403/2331 nt) arcB aerobic respiration sensor‑response protein
?NC_000913 = 3349263 NA (NA)coding (1398/2331 nt) arcB aerobic respiration sensor‑response protein
* ? NC_000913 4169328 =80 (0.500)111 (0.810)
+GGAATTAATT
75/130 0.3 61.6% noncoding (113/120 nt) rrfB 5S ribosomal RNA
?NC_000913 = 4169500 NA (NA)intergenic (+165/‑136) rrfB/murB 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase