mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 164,396 | C→T | I764I (ATC→ATT) | hrpB → | RNA‑dependent NTPase HrpB |
| JC JC | 194,729 | IS4 (+) +13 bp | intergenic (+12/‑43) | dxr → / → ispZ | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase/small regulatory RNA IspZ |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 295,882 | IS2 (+) +5 bp | coding (1211‑1215/1401 nt) | intF ← | putative phage integrase |
| RA | 414,799 | G→A | R319C (CGC→TGC) | sbcC ← | ATP‑dependent structure‑specific DNA nuclease ‑ SbcC subunit |
| RA | 448,201 | G→A | L154F (CTT→TTT) | cyoC ← | cytochrome bo3 subunit 3 |
| JC JC | 526,915 | IS1 (+) +9 bp | coding (3655‑3663/4281 nt) | rhsD → | protein RhsD |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 695,334 | T→C | H78H (CAT→CAC) | ubiF → | 3‑demethoxyubiquinol 3‑hydroxylase |
| RA | 901,135 | C→T | D134N (GAT→AAT) | artM ← | L‑arginine ABC transporter membrane subunit ArtM |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,190,053 | A→G | F132S (TTT→TCT) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| JC JC | 1,302,233 | IS1 (–) +8 bp | coding (1052‑1059/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| JC JC | 1,464,205 | IS150 (–) +3 bp | coding (667‑669/951 nt) | paaX → | DNA‑binding transcriptional repressor PaaX |
| JC JC | 1,494,484 | IS2 (+) +5 bp | coding (584‑588/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,565,745 | C→T | intergenic (‑12/+13) | dosP ← / ← dosC | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP/diguanylate cyclase DosC |
| RA | 1,594,256 | (C)8→7 | intergenic (‑1814/+4361) | hipB ← / ← lsrK | antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| JC JC | 1,743,451 | IS4 (+) +12 bp | [mdtK] | [mdtK] | |
| RA | 1,753,680 | G→A | P51S (CCT→TCT) | ydhV ← | putative oxidoreductase YdhV |
| RA | 1,817,734 | C→T | C256Y (TGT→TAT) | chbF ← | monoacetylchitobiose‑6‑phosphate hydrolase |
| RA | 1,848,239 | G→A | F146F (TTC→TTT) | ydjA ← | putative oxidoreductase YdjA |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,043,522 | C→A | noncoding (36/90 nt) | serU ← | tRNA‑Ser |
| MC JC | 2,102,944 | Δ12,095 bp | IS5‑mediated | [wbbL]–[wcaM] | [wbbL], wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, rfbA, rfbD, rfbB, galF, [wcaM] |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,286,257 | (G)5→4 | noncoding (47/77 nt) | proL → | tRNA‑Pro |
| JC JC | 2,316,421 | IS2 (+) +5 bp | coding (245‑249/651 nt) | rcsB → | DNA‑binding transcriptional activator RcsB |
| RA | 2,319,563 | A→G | L105P (CTG→CCG) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,488,630 | A→T | L180* (TTA→TAA) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| JC JC | 2,594,860 | IS4 (–) +11 bp | coding (990‑1000/2016 nt) | tmcA ← | tRNA(Met) cytidine acetyltransferase |
| JC JC | 2,736,907 | IS4 (–) +14 bp | intergenic (+24/‑234) | bamD → / → raiA | outer membrane protein assembly factor BamD/ribosome‑associated inhibitor A |
| RA | 2,777,445 | G→A | intergenic (+13/‑8) | yfjZ → / → ypjF | putative antitoxin of the YpjF‑YfjZ toxin‑antitoxin system/toxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,818,362 | G→A | intergenic (‑88/+111) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| JC JC | 3,262,447 | IS5 (+) +4 bp | intergenic (‑29/+2) | tdcE ← / ← tdcD | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4/propionate kinase |
| RA | 3,334,781 | C→T | intergenic (+100/‑128) | ispB → / → sfsB | all‑trans‑octaprenyl‑diphosphate synthase/putative transcriptional regulator SfsB |
| RA | 3,383,189 | G→A | V330V (GTG→GTA) | degS → | serine endoprotease |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,507,249 | C→T | D30N (GAC→AAC) | yhfT ← | uncharacterized protein YhfT |
| RA | 3,511,420 | C→T | M1M (ATG→ATA) † | yhfY ← | PRD domain‑containing protein YhfY |
| RA | 3,511,466 | C→T | V293V (GTG→GTA) | yhfZ ← | putative DNA‑binding transcriptional regulator YhfZ |
| RA | 3,515,876 | C→T | G13D (GGC→GAC) | dam ← | DNA adenine methyltransferase |
| RA | 3,533,565 | T→C | S250P (TCC→CCC) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,535,436 | C→T | V145I (GTA→ATA) | envZ ← | sensor histidine kinase EnvZ |
| RA | 3,535,837 | G→A | S11L (TCA→TTA) | envZ ← | sensor histidine kinase EnvZ |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,707,476 | C→A | G77V (GGC→GTC) | dppA ← | dipeptide ABC transporter periplasmic binding protein |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,775,096 | T→A | Y225N (TAC→AAC) | mtlD → | mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,775,130 | G→T | R236L (CGT→CTT) | mtlD → | mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,888,347 | G→T | intergenic (+155/‑88) | mnmE → / → tnaC | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit/tnaAB operon leader peptide |
| JC JC | 3,931,505 | IS2 (+) +5 bp | coding (190‑194/1869 nt) | kup → | K(+):H(+) symporter Kup |
| RA | 3,937,793 | C→T | P167L (CCG→CTG) | rbsK → | ribokinase |
| RA | 3,966,643 | C→T | P76L (CCT→CTT) | rho → | transcription termination factor Rho |
| RA | 3,967,134 | G→T | V240F (GTT→TTT) | rho → | transcription termination factor Rho |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,279,875 | A→T | intergenic (+47/‑105) | ghxP → / → yjcE | guanine/hypoxanthine transporter GhxP/putative transporter YjcE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,315,040 | G→T | C21* (TGC→TGA) | phnP ← | 5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,347,395 | A→T | intergenic (‑69/+9) | fumB ← / ← dcuB | fumarase B/anaerobic C4‑dicarboxylate transporter DcuB |
| RA | 4,413,516 | T→C | F163F (TTT→TTC) | yjfC → | putative acid‑‑amine ligase YjfC |
| RA | 4,423,824 | 2 bp→TT | coding (125‑126/687 nt) | ulaF → | L‑ribulose‑5‑phosphate 4‑epimerase UlaF |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 96 [0] | [0] 137 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423822–3424234 | 3424477–3424238 | 5–656 | 34 [33] | [33] 34 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 77 (0.770) | 52/590 | 0.6 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 82 (0.830) | 57/586 | 0.4 | 66.1% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 855889 = | 42 (0.420) | intergenic (‑145/‑74) | ldtB/ybiT | L,D‑transpeptidase LdtB/putative ATP‑binding protein YbiT | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 57 (0.570) | 43/586 | 1.0 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 100 (1.000) | 68/590 | 0.2 | 72.5% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 855893 | 38 (0.380) | intergenic (‑149/‑70) | ldtB/ybiT | L,D‑transpeptidase LdtB/putative ATP‑binding protein YbiT | |||||
| * | ? | NC_000913 | 1207790 = | 48 (0.480) | 78 (0.830) | 50/558 | 0.5 | 61.1% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 54 (0.570) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 52 (0.520) | 43 (0.460) | 32/558 | 1.7 | 45.5% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 54 (0.570) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 158 (1.600) | 81/582 | 0.0 | 99.7% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 96 (0.960) | 65/590 | 0.2 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 137 (1.370) | 86/590 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 3423250 = | 71 (0.710) | 42 (0.450) | 34/554 | 1.5 | 43.6% | intergenic (+56/+173) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA |
| ? | NC_000913 | = 3423417 | 42 (0.450) | intergenic (+223/+6) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA | |||||