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 |
| RA | 197,755 | G→T | G404W (GGG→TGG) | rseP → | intramembrane zinc metalloprotease RseP |
| MC JC | 295,887 | Δ85,373 bp | IS2‑mediated | [intF]–[yaiX] | 77 genes [intF], yagP, paoD, paoC, paoB, paoA, yagU, ykgJ, ecpE, ecpD, ecpC, ecpB, ecpA, matA, ykgL, ykgO, ykgM, ykgR, insE1, insF1, rclC, rclB, rclA, rclR, ykgE, ykgF, ykgG, ykgH, betA, betB, betI, betT, yahV, pdeL, yahB, yahC, yahD, yahE, yahF, yahG, yahH, yahI, yahJ, yahK, yahL, yahM, yahN, yahO, prpR, prpB, prpC, prpD, prpE, codB, codA, cynR, cynT, cynS, cynX, lacA, lacY, lacZ, lacI, mhpR, mhpA, mhpB, mhpC, mhpD, mhpF, mhpE, mhpT, yaiL, frmB, frmA, frmR, yaiO, [yaiX] |
| 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 |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 577,820 | IS2 (–) +5 bp | coding (208‑212/498 nt) | rrrD → | lysozyme |
| RA | 626,387 | C→T | S106S (AGC→AGT) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| RA | 675,824 | C→A | A242S (GCT→TCT) | ybeQ ← | Sel1 repeat‑containing protein YbeQ |
| RA | 695,334 | T→C | H78H (CAT→CAC) | ubiF → | 3‑demethoxyubiquinol 3‑hydroxylase |
| RA | 848,229 | A→T | intergenic (‑225/+179) | glnH ← / ← dps | L‑glutamine ABC transporter periplasmic binding protein/DNA protection during starvation protein |
| RA | 874,178 | Δ1 bp | coding (1200/2349 nt) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| 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 | 1,172,941 | C→A | E342* (GAA→TAA) | mfd ← | transcription‑repair coupling factor |
| RA | 1,190,053 | A→G | F132S (TTT→TCT) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| JC JC | 1,236,994 | IS2 (–) +5 bp | coding (244‑248/1533 nt) | ycgB ← | PF04293 family protein YcgB |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| 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 |
| RA | 1,494,227 | A→T | I282K (ATA→AAA) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| JC JC | 1,562,112 | IS2 (+) +5 bp | coding (366‑370/1551 nt) | ddpA ← | putative D,D‑dipeptide ABC transporter periplasmic binding protein |
| 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 | 1,638,677 | C→T | intergenic (‑10/+353) | cspI ← / ← rzpQ | cold shock‑like protein CspI/DUF2514 domain‑containing protein RzpQ |
| 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 |
| RA | 1,675,774 | G→A | A196V (GCA→GTA) | pntB ← | pyridine nucleotide transhydrogenase subunit beta |
| 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 | 2,015,663 | G→A | A262T (GCG→ACG) | fliG → | flagellar motor switch protein FliG |
| RA | 2,031,097 | (GC)4→3 | coding (1220‑1221/1419 nt) | dcm ← | DNA‑cytosine methyltransferase |
| 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 |
| 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 | 2,629,601 | IS2 (+) +5 bp | intergenic (+120/‑187) | yfgG → / → yfgH | nickel/cobalt stress response protein YfgG/lipoprotein YfgH |
| 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 |
| JC JC | 2,796,208 | IS3 (+) +3 bp | coding (535‑537/663 nt) | glaR → | DNA‑binding transcriptional repressor GlaR |
| 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 |
| RA | 2,912,586 | T→A | K356* (AAA→TAA) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,942,689 | T→C | intergenic (‑122/‑7) | gcvA ← / → gcvB | DNA‑binding transcriptional dual regulator GcvA/small regulatory RNA GcvB |
| RA | 3,334,781 | C→T | intergenic (+100/‑128) | ispB → / → sfsB | all‑trans‑octaprenyl‑diphosphate synthase/putative transcriptional regulator SfsB |
| RA | 3,472,337 | G→T | T393N (ACT→AAT) | fusA ← | elongation factor G |
| RA | 3,474,355 | G→C | Y66* (TAC→TAG) | rpsL ← | 30S ribosomal subunit protein S12 |
| 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 | 3,535,436 | C→T | V145I (GTA→ATA) | envZ ← | sensor histidine kinase EnvZ |
| RA | 3,536,106 | G→A | P160L (CCG→CTG) | ompR ← | DNA‑binding transcriptional dual regulator OmpR |
| 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 | 3,728,118 | (C)8→7 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| 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 | 3,910,755 | G→A | D257D (GAC→GAT) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,947,777 | A→G | L64P (CTA→CCA) | hdfR ← | DNA‑binding transcriptional dual regulator HdfR |
| RA | 4,000,592 | C→A | A155S (GCG→TCT) | yigE ← | DUF2233 domain‑containing protein YigE |
| RA | 4,000,594 | C→A | A155S (GCG→TCT) | yigE ← | DUF2233 domain‑containing protein YigE |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,205,882 | C→T | W17* (TGG→TAG) | purD ← | phosphoribosylamine‑‑glycine ligase |
| RA | 4,213,557 | C→T | I108I (ATC→ATT) | yjaA → | stress response protein |
| JC JC | 4,215,396 | IS5 (–) +4 bp | intergenic (+187/‑79) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,245,696 | C→A | A242S (GCC→TCC) | malE ← | maltose ABC transporter periplasmic binding protein |
| RA | 4,279,875 | Δ1 bp | 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 |
| RA | 4,429,766 | C→G | intergenic (+211/‑98) | fklB → / → cycA | peptidyl‑prolyl cis‑trans isomerase FklB/D‑serine/alanine/glycine/:H(+)symporter |
| JC JC | 4,436,762 | IS2 (+) +5 bp | coding (8‑12/741 nt) | cysQ → | 3'(2'),5'‑bisphosphate nucleotidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 29 [0] | [1] 37 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423876–3424429 | 3424429 | 1–554 | 7 [6] | [6] 7 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 39 (0.580) | 37/474 | 0.7 | 100% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 64 (0.910) | 61/490 | 0.2 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 76 (1.090) | 67/486 | 0.1 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 676358 = | 45 (0.640) | 195 (2.790) | 149/490 | 0.0 | 81.2% | coding (190/978 nt) | ybeQ | Sel1 repeat‑containing protein YbeQ |
| ? | NC_000913 | = 689045 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.310) | 21 (0.320) | 21/458 | 1.5 | 55.6% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 13 (0.200) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.330) | 37 (0.570) | 33/458 | 0.8 | 68.2% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 13 (0.200) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 29 (0.410) | 29/490 | 1.1 | 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 = | 1 (0.010) | 36 (0.510) | 33/490 | 0.9 | 97.3% | 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 | |||||