mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 177,549 | G→A | 7.0% | R26C (CGT→TGT) | yadS ← | UPF0126 family inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 262,734:1 | +G | 5.3% | coding (1232/1254 nt) | proA → | gamma‑glutamylphosphate reductase |
| RA | 265,657:2 | +C | 4.8% | coding (431/468 nt) | ykfB ← | CP4‑6 prophage, uncharacterized protein |
| RA | 762,841 | G→T | 6.8% | intergenic (+102/‑173) | sucB → / → sucC | dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit |
| RA | 876,148 | C→T | 13.8% | R272C (CGC→TGC) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,466,438 | T→G | 10.0% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,498,624 | Δ1 bp | 6.6% | intergenic (+113/‑27) | opgD → / → ydcH | OPG biosynthetic periplasmic protein/DUF465 family protein |
| RA | 1,501,720 | T→A | 8.3% | Y53* (TAT→TAA) | tehB → | tellurite, selenium methyltransferase, SAM‑dependent, tellurite, selenium resistance protein |
| RA | 1,612,932 | T→A | 5.7% | E107V (GAG→GTG) | glsB ← | glutaminase 2 |
| JC | 1,619,080 | Δ35 bp | 25.9% | intergenic (‑172/‑6) | marC ← / → marR | UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance |
| RA | 1,936,648 | C→T | 62.2% | intergenic (‑334/‑4) | zwf ← / → yebK | glucose‑6‑phosphate 1‑dehydrogenase/putative DNA‑binding transcriptional regulator |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,151,859 | A→G | 9.5% | F205S (TTT→TCT) | yegK ← | ser/thr phosphatase‑related protein |
| JC | 2,413,511 | Δ10 bp | 19.6% | coding (44‑53/1203 nt) | ackA → | acetate kinase A and propionate kinase 2 |
| JC | 2,526,109 | Δ3 bp | 5.1% | coding (744‑746/927 nt) | yfeR ← | transcriptional regulator of yefH |
| RA | 3,213,424 | T→G | 41.1% | I127S (ATC→AGC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,361,439 | C→T | 13.8% | A89V (GCA→GTA) | gltF → | periplasmic protein |
| RA | 3,627,312 | T→C | 3.7% | K742K (AAA→AAG) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,729,753 | A→G | 6.3% | F338L (TTC→CTC) | xylA ← | D‑xylose isomerase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,855,800 | A→T | 4.3% | L57H (CTC→CAC) | yidG ← | inner membrane protein |
| RA | 3,955,141 | C→G | 4.8% | G555G (GGC→GGG) | ilvD → | dihydroxyacid dehydratase |
| JC | 4,001,644 | Δ5 bp | 95.4% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,011,943 | A→T | 5.8% | D290V (GAT→GTT) D291E (GAT→GAA) |
yigM → metR ← |
putative inner membrane EamA‑like transporter methionine biosynthesis regulon transcriptional regulator |
| JC | 4,049,990 | Δ12 bp | 40.7% | noncoding (93‑104/109 nt) | spf → | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| RA | 4,157,049 | A→G | 5.4% | E67E (GAA→GAG) | argH → | argininosuccinate lyase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| JC | 4,189,443:1 | +TAC | 5.8% | coding (4095/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,285,466 | A→G | 4.3% | P635P (CCT→CCC) | acs ← | acetyl‑CoA synthetase |
| RA | 4,296,189 | A→G | 29.1% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 31.5% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 16.0% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,285 | C→T | 7.4% | intergenic (+492/+152) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,302,793 | T→A | 4.5% | K96I (AAA→ATA) | mdtO ← | membrane translocase (MDR) of MdtNOP efflux pump, PET family |
| RA | 4,308,356 | G→T | 21.7% | L42M (CTG→ATG) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
| RA | 4,326,049 | G→A | 7.3% | intergenic (‑307/+351) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,089 | T→G | 13.4% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,629,275 | T→G | 5.8% | I417L (ATC→CTC) | ettA ← | energy‑dependent translational throttle A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2990842 | 2991368 | 527 | 20 [15] | [15] 16 | [ygeF]–[ygeG] | [ygeF], ygeF, [ygeG] |
| * | * | ÷ | NC_000913 | 3423892–3424231 | 3424400–3424237 | 7–509 | 17 [15] | [15] 17 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4233699 | 4235427 | 1729 | 16 [15] | [14] 16 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 58 (0.960) | 50/506 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 1 (0.020) | 41 (0.690) | 37/500 | NT | 97.6% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 0 (0.000) | 54 (0.910) | 42/498 | NT | 100% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.280) | 29 (0.510) | 28/474 | NT | 64.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 16 (0.280) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.270) | 47 (0.830) | 40/474 | NT | 75.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.280) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 53 (0.880) | 44/506 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 9 (0.150) | 9/506 | NT | 18.0% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | NC_000913 | = 2101469 | 41 (0.680) | pseudogene (276/349 nt) | wbbL | pseudogene, lipopolysaccharide biosynthesis protein | |||||
| * | ? | NC_000913 | = 1840621 | 75 (1.250) | 4 (0.070) | 4/500 | NT | 6.1% | coding (1155/1308 nt) | ynjE | molybdopterin synthase sulfurtransferase |
| ? | NC_000913 | = 1841095 | 50 (0.840) | coding (309/621 nt) | ynjF | CDP‑alcohol phosphatidyltransferase family inner membrane protein | |||||
| * | ? | NC_000913 | 1928538 = | 53 (0.880) | 4 (0.070) | 3/492 | NT | 6.8% | coding (302/2061 nt) | ptrB | protease II |
| ? | NC_000913 | 1928806 = | 58 (0.990) | coding (34/2061 nt) | ptrB | protease II | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 31 (0.520) | 24/506 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 39 (0.650) | 29/506 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 3135411 | 66 (1.100) | 4 (0.070) | 3/488 | NT | 5.3% | coding (959/1500 nt) | pitB | phosphate transporter |
| ? | NC_000913 | = 3135484 | 78 (1.340) | coding (886/1500 nt) | pitB | phosphate transporter | |||||
| * | ? | NC_000913 | 3542826 = | 86 (1.430) | 3 (0.050) | 3/496 | NT | 3.7% | coding (101/237 nt) | feoC | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | 3543063 = | 70 (1.190) | intergenic (+101/‑102) | feoC/yhgA | putative DNA‑binding transcriptional regulator/transposase_31 family protein | |||||
| * | ? | NC_000913 | 4049857 = | 7 (0.120) | 37 (0.620) | 32/504 | NT | 84.1% | intergenic (+106/‑41) | polA/spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | 4498183 = | NA (NA) | intergenic (+242/‑90) | intB/insC1 | pseudogene, integrase homology,IS, phage, Tn, Phage‑related functions and prophages, KpLE2 phage‑like element, P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | NC_000913 | = 4049863 | 7 (0.120) | 30 (0.500) | 27/504 | NT | 81.1% | intergenic (+112/‑35) | polA/spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | = 4499511 | NA (NA) | intergenic (+10/+83) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||