mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 187,969 | C→A | 7.8% | D228Y (GAT→TAT) | glnD ← | uridylyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 279,281 | T→C | 7.2% | Q134R (CAG→CGG) | insB1 ← | IS1 transposase B |
| RA | 541,524:1 | +A | 6.2% | coding (960/1302 nt) | ybbY → | putative uracil/xanthine transporter |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,334,015 | A→G | 58.5% | K54R (AAG→AGG) | cysB → | N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor |
| RA | 1,967,541 | T→A | 6.0% | M321L (ATG→TTG) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| JC JC | 2,097,812 | IS5 (–) +4 bp | 56.8% | coding (487‑490/981 nt) | wzzB ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| JC | 2,121,524 | Δ4 bp | 9.6% | coding (28‑31/1395 nt) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| JC JC | 2,876,678 | IS5 (+) +4 bp | 12.7% | coding (98‑101/1038 nt) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 3,400,526 | G→A | 7.4% | R188C (CGC→TGC) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,640,511 | T→C | 5.1% | M134T (ATG→ACG) | uspA → | universal stress global response regulator |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,968,509 | Δ1 bp | 9.3% | coding (594/1104 nt) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| JC | 3,976,197 | Δ9 bp | 7.0% | coding (1052‑1060/1131 nt) | wecE → | TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| JC | 4,180,661 | +GCT | 61.6% | coding (102/366 nt) | rplL → | 50S ribosomal subunit protein L7/L12 |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,267,780 | G→A | 6.2% | E223K (GAA→AAA) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,296,190 | A→G | 26.2% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 25.4% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 16.7% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583130 | 584734 | 1605 | 28 [26] | [26] 28 | [tfaX]–[ompT] | [tfaX],appY,[ompT] |
| * | * | ÷ | NC_000913 | 1211062 | 1212808 | 1747 | 28 [27] | [27] 28 | [mcrA]–[ycgX] | [mcrA],icdC,iraM,[ycgX] |
| * | * | ÷ | NC_000913 | 1215950 | 1216802 | 853 | 28 [27] | [26] 28 | [ycgZ]–[ymgC] | [ycgZ],ymgA,ariR,[ymgC] |
| * | * | ÷ | NC_000913 | 1299468 | 1300729 | 1262 | 28 [27] | [27] 29 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1529944 | 1530473 | 530 | 28 [27] | [27] 28 | [ydcD] | [ydcD] |
| * | * | ÷ | NC_000913 | 1978495 | 1979278 | 784 | 28 [26] | [4] 30 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 2455600 | 2456192 | 593 | 29 [27] | [24] 29 | [yfcV] | [yfcV] |
| * | * | ÷ | NC_000913 | 2774335 | 2775168 | 834 | 28 [27] | [26] 28 | [yfjW] | [yfjW] |
| * | * | ÷ | NC_000913 | 2785821 | 2786593 | 773 | 28 [27] | [27] 28 | [ileY]–[ygaQ] | [ileY],[ygaQ] |
| * | * | ÷ | NC_000913 | 2990617 | 2991428 | 812 | 28 [26] | [26] 28 | [ygeF]–[ygeG] | [ygeF],ygeF,[ygeG] |
| * | * | ÷ | NC_000913 | 2994932 | 2996010 | 1079 | 33 [27] | [27] 30 | [ygeK]–[ygeO] | [ygeK],ygeN,[ygeN],[ygeO] |
| * | * | ÷ | NC_000913 | 3268714 | 3269646 | 933 | 28 [27] | [27] 28 | [yhaC] | [yhaC] |
| * | * | ÷ | NC_000913 | 3769496 | 3770107 | 612 | 30 [27] | [27] 28 | [yibV]–[yibU] | [yibV],yibV,yibU,[yibU] |
| * | * | ÷ | NC_000913 | 3796824 | 3797413 | 590 | 31 [27] | [26] 29 | [waaC]–[waaL] | [waaC],[waaL] |
| * | * | ÷ | NC_000913 | 3798472 | 3800257 | 1786 | 28 [26] | [27] 29 | [waaU]–waaZ | [waaU],waaZ |
| * | * | ÷ | NC_000913 | 3804100 | 3805234 | 1135 | 28 [24] | [27] 29 | [waaB]–[waaP] | [waaB],waaS,[waaP] |
| * | * | ÷ | NC_000913 | 4476510 | 4477189 | 680 | 32 [26] | [27] 28 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| * | * | ÷ | NC_000913 | 4556315 | 4556782 | 468 | 35 [24] | [26] 29 | [yjiC] | [yjiC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 26 (0.320) | 61 (0.810) | 46/468 | NT | 68.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 33 (0.440) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 26 (0.320) | 46 (0.610) | 37/468 | NT | 61.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 33 (0.440) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 20 (0.250) | 17/492 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 24 (0.310) | 20/484 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 6 (0.080) | 6/494 | NT | 8.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2913666 | 62 (0.780) | intergenic (‑15/+33) | relA/rlmD | (p)ppGpp synthetase I/GTP pyrophosphokinase/23S rRNA m(5)U1939 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | 2642945 = | 45 (0.560) | 6 (0.070) | 6/500 | NT | 11.8% | intergenic (‑101/+184) | rodZ/rlmN | MreB assembly cytoskeletal protein/dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent |
| ? | NC_000913 | = 3187426 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2876678 = | 57 (0.710) | 4 (0.050) | 4/500 | NT | 6.6% | coding (98/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 5 (0.060) | 5/500 | NT | 27.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3802089 = | 13 (0.160) | coding (970/1020 nt) | waaO | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase | |||||