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 | freq | annotation | gene | description |
| RA | 53,376 | G→A | 12.0% | P14L (CCC→CTC) | pdxA ← | 4‑hydroxythreonine‑4‑phosphate dehydrogenase |
| RA | 53,379 | T→C | 13.0% | E13G (GAG→GGG) | pdxA ← | 4‑hydroxythreonine‑4‑phosphate dehydrogenase |
| RA | 77,372 | A→G | 6.5% | noncoding (6/227 nt) | sgrS → | small regulatory RNA SgrS |
| RA | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 151,519 | A→C | 12.4% | I27M (ATT→ATG) | yadK ← | putative fimbrial protein YadK |
| RA | 151,522 | G→T | 13.8% | A26A (GCC→GCA) | yadK ← | putative fimbrial protein YadK |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 285,882 | T→G | 9.5% | I163S (ATC→AGC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 285,887 | C→A | 6.8% | L165M (CTG→ATG) | yagG → | putative D‑xylonate transporter YagG |
| RA | 314,258 | G→A | 10.2% | intergenic (‑453/‑99) | ykgP ← / → eaeH | putative oxidoreductase/putative porin domain‑containing protein EaeH |
| RA | 493,634 | G→A | 8.0% | A515T (GCA→ACA) | dnaX → | DNA polymerase III subunit tau |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 699,556 | C→T | 7.6% | intergenic (‑379/+18) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 699,559 | A→G | 7.7% | intergenic (‑382/+15) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 710,595 | G→T | 100% | P18T (CCT→ACT) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 800,807 | G→T | 100% | A17S (GCG→TCG) | ybhH → | putative isomerase YbhH |
| RA | 800,934 | A→G | 13.1% | K59R (AAA→AGA) | ybhH → | putative isomerase YbhH |
| RA | 940,751 | T→C | 13.4% | intergenic (+31/‑208) | serS → / → dmsA | serine‑‑tRNA ligase/dimethyl sulfoxide reductase subunit A |
| RA | 940,754 | G→A | 13.6% | intergenic (+34/‑205) | serS → / → dmsA | serine‑‑tRNA ligase/dimethyl sulfoxide reductase subunit A |
| RA | 958,771 | A→T | 10.2% | intergenic (+30/‑41) | serC → / → aroA | phosphoserine/phosphohydroxythreonine aminotransferase/3‑phosphoshikimate 1‑carboxyvinyltransferase |
| RA | 962,670 | A→G | 22.7% | K226E (AAA→GAA) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,019,309 | C→A | 27.8% | D249Y (GAT→TAT) | ompA ← | outer membrane porin A |
| RA | 1,177,646 | T→G | 11.3% | N109K (AAT→AAG) | lolE → | lipoprotein release complex ‑ inner membrane subunit |
| RA | 1,177,647 | C→A | 10.8% | L110I (CTT→ATT) | lolE → | lipoprotein release complex ‑ inner membrane subunit |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,471,425 | A→G | 10.8% | pseudogene (907/3495 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 1,999,460 | G→T | 16.5% | T7T (ACC→ACA) | dcyD ← | D‑cysteine desulfhydrase |
| RA | 2,090,122 | A→G | 9.7% | intergenic (+76/‑70) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,124 | C→G | 9.5% | intergenic (+78/‑68) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,090,126 | C→T | 9.7% | intergenic (+80/‑66) | hisL → / → hisG | his operon leader peptide/ATP phosphoribosyltransferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,391,417 | C→G | 7.5% | W30S (TGG→TCG) | nuoN ← | NADH:quinone oxidoreductase subunit N |
| JC | 2,392,615 | Δ3 bp | 57.0% | coding (425‑427/1530 nt) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,414,689 | C→G | 12.9% | intergenic (+17/‑58) | ackA → / → pta | acetate kinase/phosphate acetyltransferase |
| RA | 2,575,770 | G→A | 10.0% | P12P (CCC→CCT) | eutS ← | putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,843,708 | T→A | 7.6% | H168L (CAC→CTC) | hycG ← | formate hydrogenlyase subunit HycG |
| RA | 2,972,652 | A→T | 10.4% | intergenic (+15/+17) | tas → / ← lplT | putative NADP(H)‑dependent aldo‑keto reductase Tas/lysophospholipid transporter |
| RA | 2,972,653 | A→T | 7.4% | intergenic (+16/+16) | tas → / ← lplT | putative NADP(H)‑dependent aldo‑keto reductase Tas/lysophospholipid transporter |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,091,709 | G→A | 13.5% | L192L (CTG→CTA) | rsmE → | 16S rRNA m(3)U1498 methyltransferase |
| RA | 3,142,885 | A→G | 8.1% | G35G (GGT→GGC) | hybC ← | hydrogenase 2 large subunit |
| RA | 3,156,591 | T→G | 7.8% | intergenic (+73/‑32) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,288,033 | T→G | 9.2% | intergenic (+23/‑57) | yraH → / → yraI | putative fimbrial protein YraH/putative fimbrial chaperone YraI |
| RA | 3,332,822 | G→A | 9.4% | intergenic (‑87/+40) | yhbE ← / ← rpmA | inner membrane protein YhbE/50S ribosomal subunit protein L27 |
| RA | 3,332,823 | T→C | 11.7% | intergenic (‑88/+39) | yhbE ← / ← rpmA | inner membrane protein YhbE/50S ribosomal subunit protein L27 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,642,358 | T→A | 6.3% | intergenic (+27/+22) | dtpB → / ← rsmJ | dipeptide/tripeptide:H(+) symporter DtpB/16S rRNA m(2)G1516 methyltransferase |
| RA | 3,729,405 | C→G | 8.6% | intergenic (‑34/+38) | xylB ← / ← xylA | xylulokinase/xylose isomerase |
| RA | 3,729,408 | C→G | 8.8% | intergenic (‑37/+35) | xylB ← / ← xylA | xylulokinase/xylose isomerase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,817,949 | A→C | 7.5% | I64L (ATC→CTC) | dinD → | DNA damage‑inducible protein D |
| RA | 3,817,957 | T→A | 8.8% | D66E (GAT→GAA) | dinD → | DNA damage‑inducible protein D |
| RA | 3,832,188 | A→T | 12.3% | intergenic (+22/+31) | yicH → / ← yicI | AsmA famly protein YicH/alpha‑D‑xyloside xylohydrolase |
| RA | 3,832,191 | C→G | 8.2% | intergenic (+25/+28) | yicH → / ← yicI | AsmA famly protein YicH/alpha‑D‑xyloside xylohydrolase |
| RA | 3,832,194 | A→T | 8.8% | intergenic (+28/+25) | yicH → / ← yicI | AsmA famly protein YicH/alpha‑D‑xyloside xylohydrolase |
| RA | 3,981,102 | T→A | 11.5% | V72V (GTT→GTA) | yifK → | putative transporter YifK |
| RA | 3,989,940 | C→T | 10.4% | R276H (CGC→CAC) | hemC ← | hydroxymethylbilane synthase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,002,902 | A→T | 5.0% | S98T (TCA→ACA) | yigG ← | inner membrane protein |
| RA | 4,002,903 | A→T | 5.0% | C97* (TGT→TGA) | yigG ← | inner membrane protein |
| RA | 4,028,910 | G→C | 11.1% | Q688E (CAG→GAG) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,082,696 | G→C | 11.3% | Q22E (CAG→GAG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | 4,114,431 | G→A | 100% | N14N (AAC→AAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,123,110 | G→A | 100% | P77L (CCA→CTA) | ftsN ← | cell division protein FtsN |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,189,573 | A→C | 5.9% | *1408Y (TAA→TAC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,296,060 | C→T | 28.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,323,313 | G→C | 5.7% | intergenic (‑32/+23) | phnE ← / ← phnD | phosphonate ABC transporter membrane subunit/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,376,280 | G→A | 8.4% | intergenic (+15/‑37) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,376,291 | T→C | 6.8% | intergenic (+26/‑26) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,424,468 | A→C | 6.9% | intergenic (+82/+48) | ulaF → / ← yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY |
| RA | 4,426,592 | T→A | 9.1% | intergenic (+35/+36) | rplI → / ← yjfZ | 50S ribosomal subunit protein L9/protein YjfZ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423761–3424528 | 3424528 | 1–768 | 16 [14] | [12] 17 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225154 = | NA (NA) | 4 (0.090) | 4/254 | NT | NA | noncoding (1384/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225176 = | NA (NA) | noncoding (1406/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 315520 | NA (NA) | 3 (0.070) | 3/250 | NT | NA | noncoding (292/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315537 | NA (NA) | noncoding (309/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315563 = | NA (NA) | 4 (0.100) | 3/244 | NT | NA | noncoding (335/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315599 = | NA (NA) | noncoding (371/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315572 | NA (NA) | 7 (0.170) | 6/244 | NT | NA | noncoding (344/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315588 | NA (NA) | noncoding (360/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315695 | NA (NA) | 3 (0.070) | 3/252 | NT | NA | noncoding (467/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315719 | NA (NA) | noncoding (491/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 315852 | NA (NA) | 44 (1.000) | 11/256 | NT | NA | noncoding (624/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315875 | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 349606 = | NA (NA) | 4 (0.090) | 4/250 | NT | NA | noncoding (1/36 nt) | other | REP25a |
| ? | NC_000913 | 349636 = | NA (NA) | noncoding (31/36 nt) | other | REP25a | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 3 (0.070) | 3/246 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 412958 = | 39 (0.860) | 3 (0.070) | 3/252 | NT | 7.1% | coding (2796/3147 nt) | sbcC | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| ? | NC_000913 | 412982 = | 41 (0.940) | coding (2772/3147 nt) | sbcC | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit | |||||
| * | ? | NC_000913 | 433694 = | 41 (0.900) | 4 (0.090) | 3/250 | NT | 9.8% | coding (240/1104 nt) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| ? | NC_000913 | 433734 = | 35 (0.810) | coding (280/1104 nt) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase | |||||
| * | ? | NC_000913 | 463830 = | 52 (1.140) | 3 (0.070) | 3/250 | NT | 5.9% | intergenic (+44/‑107) | ppiD/ybaV | periplasmic folding chaperone/helix‑hairpin‑helix 3 family protein |
| ? | NC_000913 | 463856 = | 46 (1.070) | intergenic (+70/‑81) | ppiD/ybaV | periplasmic folding chaperone/helix‑hairpin‑helix 3 family protein | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2491 (55.190) | 255/262 | NT | 98.4% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 40 (0.880) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 40 (0.880) | 11 (0.330) +34 bp |
8/196 | NT | 33.1% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 20 (0.440) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 3 (0.070) | 19 (0.480) | 18/232 | NT | 73.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.280) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 4 (0.090) | 22 (0.550) | 21/232 | NT | 75.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.280) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1314673 = | 37 (0.810) | 3 (0.070) | 3/246 | NT | 8.0% | intergenic (+15/+45) | ompW/yciE | outer membrane protein W/DUF892 domain‑containing protein YciE |
| ? | NC_000913 | 1314694 = | 35 (0.830) | intergenic (+36/+24) | ompW/yciE | outer membrane protein W/DUF892 domain‑containing protein YciE | |||||
| * | ? | NC_000913 | 1552011 = | 63 (1.390) | 4 (0.090) | 4/248 | NT | 6.3% | intergenic (+20/+387) | fdnI/yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM |
| ? | NC_000913 | 1552221 = | NA (NA) | intergenic (+230/+177) | fdnI/yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM | |||||
| * | ? | NC_000913 | 1914760 = | 48 (1.060) | 3 (0.070) | 3/244 | NT | 6.5% | coding (57/2049 nt) | prc | tail‑specific protease |
| ? | NC_000913 | 1914786 = | 42 (1.000) | coding (31/2049 nt) | prc | tail‑specific protease | |||||
| * | ? | NC_000913 | = 1922031 | 42 (0.920) | 4 (0.090) | 4/252 | NT | 9.1% | intergenic (+15/‑90) | yebV/yebW | protein YebV/protein YebW |
| ? | NC_000913 | = 1922040 | 40 (0.920) | intergenic (+24/‑81) | yebV/yebW | protein YebV/protein YebW | |||||
| * | ? | NC_000913 | = 2064765 | 33 (0.730) | 3 (0.070) | 3/254 | NT | 8.4% | coding (458/744 nt) | cobS | cobalamin 5'‑phosphate synthase |
| ? | NC_000913 | = 2064780 | 34 (0.780) | coding (443/744 nt) | cobS | cobalamin 5'‑phosphate synthase | |||||
| * | ? | NC_000913 | = 3110452 | 43 (0.950) | 4 (0.090) | 3/260 | NT | 8.8% | intergenic (+11/+138) | pheV/yghD | tRNA‑Phe/putative type II secretion system M‑type protein |
| ? | NC_000913 | = 3110475 | 41 (0.920) | intergenic (+34/+115) | pheV/yghD | tRNA‑Phe/putative type II secretion system M‑type protein | |||||
| * | ? | NC_000913 | 3322035 = | 71 (1.560) | 4 (0.090) | 4/254 | NT | 5.4% | intergenic (‑422/+37) | yhbX/leuU | putative hydrolase, inner membrane/tRNA‑Leu |
| ? | NC_000913 | 3322065 = | 72 (1.650) | intergenic (‑452/+7) | yhbX/leuU | putative hydrolase, inner membrane/tRNA‑Leu | |||||
| * | ? | NC_000913 | 3525479 = | NA (NA) | 3 (0.070) | 3/248 | NT | NA | noncoding (1/34 nt) | other | REP251a |
| ? | NC_000913 | 3525507 = | NA (NA) | noncoding (29/34 nt) | other | REP251a | |||||
| * | ? | NC_000913 | 3690179 = | 53 (1.170) | 3 (0.070) | 3/250 | NT | 5.5% | coding (83/1107 nt) | bcsZ | endo‑1,4‑D‑glucanase |
| ? | NC_000913 | 3690205 = | 52 (1.210) | coding (57/1107 nt) | bcsZ | endo‑1,4‑D‑glucanase | |||||
| * | ? | NC_000913 | 3754861 = | NA (NA) | 3 (0.070) | 3/250 | NT | NA | noncoding (1/34 nt) | other | REP270a |
| ? | NC_000913 | 3754889 = | NA (NA) | noncoding (29/34 nt) | other | REP270a | |||||
| * | ? | NC_000913 | = 3854888 | 43 (0.950) | 5 (0.120) | 5/246 | NT | 10.9% | coding (967/1185 nt) | emrD | multidrug efflux pump EmrD |
| ? | NC_000913 | = 3854930 | 42 (0.990) | coding (1009/1185 nt) | emrD | multidrug efflux pump EmrD | |||||
| * | ? | NC_000913 | = 4168341 | 13 (0.290) | 3 (0.070) | 3/244 | NT | 19.4% | intergenic (+141/‑31) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| ? | NC_000913 | = 4168363 | 13 (0.310) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu | |||||
| * | ? | NC_000913 | 4257736 = | 45 (0.990) | 3 (0.070) | 3/250 | NT | 6.4% | intergenic (+13/‑6) | lexA/dinF | DNA‑binding transcriptional repressor LexA/DNA damage‑inducible protein F |
| ? | NC_000913 | 4257762 = | 45 (1.050) | coding (21/1380 nt) | dinF | DNA damage‑inducible protein F | |||||