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 | 412,627 | T→G | S1043R (AGT→CGT) | sbcC ← | ATP‑dependent structure‑specific DNA nuclease ‑ SbcC subunit |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| RA | 627,422 | G→T | L451L (CTG→CTT) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase |
| MC JC | 687,775 | Δ76 bp | IS5‑mediated | gltI ← / ← insH3 | glutamate/aspartate ABC transporter periplasmic binding protein/IS5 family transposase and trans‑activator |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| JC JC | 1,217,340 | IS2 (–) +5 bp | coding (13‑17/1524 nt) | pdeG → | putative c‑di‑GMP phosphodiesterase PdeG |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,910,070 | A→C | P10P (CCT→CCG) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| RA | 1,960,601 | C→A | N180K (AAC→AAA) | argS → | arginine‑‑tRNA ligase |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,173,624 | IS1 (+) +8 bp | intergenic (‑751/+651) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC | 2,175,887 | (CAGCA)1→2 | coding (435/1263 nt) | gatZ ← | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,600,467 | G→T | G188* (GGA→TGA) | gcvR → | putative transcriptional regulator GcvR |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,957,757 | G→T | L376L (CTC→CTA) | ptrA ← | protease 3 |
| RA | 2,990,625 | G→T | intergenic (‑265/‑643) | yqeK ← / → ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| RA | 3,240,844 | G→A | A301T (GCG→ACG) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,285,660 | C→A | L61L (CTC→CTA) | agaD → | galactosamine‑specific PTS enzyme IID component |
| JC JC | 3,412,814 | IS5 (+) +4 bp | coding (649‑652/663 nt) | envR ← | DNA‑binding transcriptional repressor EnvR |
| RA | 3,500,818 | G→T | Q303H (CAG→CAT) | frlA → | fructoselysine/psicoselysine transporter |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,682,927 | (A)5→6 | coding (521/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| MC JC | 3,931,163 | Δ10 bp | intergenic (‑70/‑144) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 4,184,050 | C→A | R936S (CGC→AGC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,430,485 | C→A | P208T (CCG→ACG) | cycA → | D‑serine/alanine/glycine/:H(+)symporter |
| RA | 4,503,622 | C→A | intergenic (‑191/‑436) | insG ← / → nanX | IS4 family putative transposase/sialic acid transporter NanX |
| RA | 4,616,669 | G→T | L133I (CTA→ATA) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1299495–1300693 | 1300693 | 1–1199 | 94 [0] | [2] 67 | insH21 | insH21 |
| * | * | ÷ | NC_000913 | 3423880–3424433 | 3424433 | 1–554 | 16 [15] | [15] 16 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035354–4035733 | 4036891–4035735 | 3–1538 | 16 [15] | [15] 16 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 16974 = | 17 (0.140) | 47 (0.390) | 46/480 | 1.4 | 73.4% | noncoding (23/59 nt) | sokC | small regulatory RNA antitoxin SokC |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 16975 | 16 (0.130) | 64 (0.530) +GG |
57/476 | 1.0 | 80.1% | noncoding (24/59 nt) | sokC | small regulatory RNA antitoxin SokC |
| ? | NC_000913 | = 3722076 | NA (NA) | intergenic (+27/+252) | insK/glyS | IS150 family conserved protein InsB/glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_000913 | = 16976 | 13 (0.110) | 83 (0.690) | 76/474 | 0.5 | 86.5% | noncoding (25/59 nt) | sokC | small regulatory RNA antitoxin SokC |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 59123 = | 18 (0.150) | 31 (0.250) | 28/480 | 2.5 | 63.3% | coding (650/651 nt) coding (3/159 nt) |
yabP yabQ |
putative uncharacterized protein YabP protein YabQ |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 59125 | 18 (0.150) | 61 (0.500) | 56/478 | 1.0 | 77.3% | coding (5/159 nt) | yabQ | protein YabQ |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 94 (0.800) | 83/464 | 0.4 | 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 | 257908 = | NA (NA) | 94 (0.770) | 83/480 | 0.4 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1299494 | 0 (0.000) | intergenic (+249/‑73) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 60 (0.490) | 56/480 | 1.0 | 73.2% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 890625 = | 22 (0.180) | coding (129/258 nt) | grxA | reduced glutaredoxin 1 | |||||
| * | ? | NC_000913 | = 566774 | 120 (0.990) | 81 (0.670) | 38/476 | 1.8 | 42.7% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 98 (0.810) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 689045 | NA (NA) | 26 (0.210) | 25/478 | 2.7 | 21.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 733318 | 95 (0.780) | coding (3736/4194 nt) | rhsC | rhs element protein RhsC | |||||
| * | ? | NC_000913 | = 890629 | 18 (0.150) | 74 (0.610) | 69/480 | 0.7 | 80.4% | coding (125/258 nt) | grxA | reduced glutaredoxin 1 |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 64 (0.530) | 35 (0.310) | 34/448 | 1.9 | 42.0% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 37 (0.330) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.390) | 70 (0.620) | 65/448 | 0.7 | 63.1% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 37 (0.330) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | 1269977 = | 28 (0.230) | 43 (0.360) | 38/476 | 1.8 | 60.6% | intergenic (+54/+261) | rdlB/ldrC | putative antisense regulatory RNA RdlB/small toxic polypeptide LdrC |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 1269980 | 26 (0.210) | 47 (0.390) | 45/480 | 1.5 | 64.4% | intergenic (+57/+258) | rdlB/ldrC | putative antisense regulatory RNA RdlB/small toxic polypeptide LdrC |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 1300694 = | 2 (0.020) | 65 (0.550) +CACTTTCC |
57/464 | 1.0 | 97.1% | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1411899 = | 34 (0.280) | 90 (0.830) | 79/428 | 0.4 | 78.5% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 19 (0.180) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 1411924 | 45 (0.370) | 41 (0.380) | 39/428 | 1.5 | 58.1% | coding (25/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | 1434985 = | 19 (0.180) | intergenic (‑579/+200) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 33 (0.270) | 32/480 | 2.2 | 42.3% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1590448 | 45 (0.370) | intergenic (‑447/+406) | ydeT/hipA | fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 28 (0.230) | 28/476 | 2.4 | 32.2% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 3991038 = | 59 (0.490) | intergenic (‑272/‑115) | hemC/cyaA | hydroxymethylbilane synthase/adenylate cyclase | |||||
| * | ? | NC_000913 | 1492142 = | 34 (0.280) | 62 (0.510) | 58/480 | 1.0 | 64.6% | noncoding (24/57 nt) | sokB | putative small regulatory RNA antitoxin SokB |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 1492144 | 37 (0.300) | 58 (0.480) | 53/474 | 1.1 | 61.4% | noncoding (26/57 nt) | sokB | putative small regulatory RNA antitoxin SokB |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 1590444 = | 46 (0.380) | 48 (0.390) | 43/480 | 1.5 | 51.1% | intergenic (‑443/+410) | ydeT/hipA | fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1596405 = | 32 (0.260) | 42 (0.340) | 39/480 | 1.7 | 56.8% | intergenic (‑3963/+2212) | hipB/lsrK | antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase |
| ? | NC_000913 | = 2070271 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1596409 | 31 (0.250) | 46 (0.380) | 44/480 | 1.5 | 59.7% | intergenic (‑3967/+2208) | hipB/lsrK | antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2521129 | 1 (0.010) | 47 (0.590) | 44/312 | 0.7 | 98.3% | intergenic (+3/‑44) | valX/valY | tRNA‑Val/tRNA‑Val |
| ? | NC_000913 | 2521252 = | 1 (0.010) | intergenic (+4/‑1) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 3099402 | 20 (0.160) | 65 (0.530) | 59/480 | 1.0 | 76.5% | coding (164/1008 nt) | yggM | DUF1202 domain‑containing protein YggM |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 65 (0.530) | 59/480 | 1.0 | 54.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3346175 | 55 (0.450) | coding (3/288 nt) | hpf | ribosome hibernation‑promoting factor | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 64 (0.530) | 59/476 | 0.9 | 52.9% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3346171 = | 57 (0.470) | intergenic (+21/‑2) | rpoN/hpf | RNA polymerase sigma factor RpoN/ribosome hibernation‑promoting factor | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 43 (0.360) | 40/474 | 1.7 | 56.7% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4269492 = | 33 (0.270) | coding (79/714 nt) | aphA | acid phosphatase/phosphotransferase | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 88 (0.720) | 79/480 | 0.5 | 73.3% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4365462 = | 32 (0.260) | intergenic (‑106/+10) | cutA/dcuA | copper binding protein CutA/C4‑dicarboxylate transporter DcuA | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 77 (0.630) | 70/480 | 0.7 | 53.1% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4424481 = | 68 (0.560) | intergenic (+95/+35) | ulaF/yjfY | L‑ribulose‑5‑phosphate 4‑epimerase UlaF/DUF1471 domain‑containing protein YjfY | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 32 (0.260) | 31/478 | 2.2 | 22.8% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4430711 = | 109 (0.900) | coding (848/1413 nt) | cycA | D‑serine/alanine/glycine/:H(+)symporter | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 78 (0.640) | 70/480 | 0.7 | 30.8% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4452691 = | 175 (1.440) | coding (121/1026 nt) | ytfT | galactofuranose ABC transporter putative membrane subunit YtfT | |||||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 53 (0.440) | 49/478 | 1.3 | 62.5% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 4269494 | 32 (0.260) | coding (81/714 nt) | aphA | acid phosphatase/phosphotransferase | |||||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 51 (0.420) | 50/478 | 1.2 | 56.7% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 4365464 | 39 (0.320) | intergenic (‑108/+8) | cutA/dcuA | copper binding protein CutA/C4‑dicarboxylate transporter DcuA | |||||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 85 (0.700) | 76/478 | 0.5 | 43.8% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 4430713 | 109 (0.900) | coding (850/1413 nt) | cycA | D‑serine/alanine/glycine/:H(+)symporter | |||||
| * | ? | NC_000913 | 4365920 = | 105 (0.860) | 34 (0.280) | 32/480 | 2.2 | 24.5% | coding (854/1302 nt) | dcuA | C4‑dicarboxylate transporter DcuA |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||