mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 3,875,521 | 0 | T→C | 23.0% | 28.8 ‑9.2 ‑0.0 | 75 | A28A (GCT→GCC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,522 | 0 | C→G | 22.7% | 26.1 ‑10.1 0.0 | 75 | L29V (CTG→GTG) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,524 | 0 | G→C | 14.5% | 19.3 ‑6.1 0.0 | 77 | L29L (CTG→CTC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,529 | 0 | C→G | 12.0% | 14.9 ‑5.6 0.0 | 75 | S31C (TCC→TGC) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,532 | 0 | A→T | 19.5% | 12.8 ‑9.8 ‑0.0 | 77 | H32L (CAT→CTT) | yidX | putative lipoprotein |
| * | NC_000913 | 3,875,525 | 0 | G→T | 18.2% | 10.0 ‑8.4 ‑0.0 | 77 | V30F (GTT→TTT) | yidX | putative lipoprotein |
| * | NC_000913 | 4,476,987 | 0 | T→. | 100.0% | 4.1 | 1 | coding (1551/1815 nt) | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| * | NC_000913 | 4,476,988 | 0 | T→. | 100.0% | 4.1 | 1 | coding (1552/1815 nt) | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| * | NC_000913 | 237,254 | 0 | A→C | 100.0% | 1.5 | 1 | intergenic (+247/‑81) | aspV/yafT | tRNA‑Asp/lipoprotein |
| * | NC_000913 | 4,037,286 | 0 | C→A | 100.0% | 1.3 | 1 | noncoding (27/76 nt) | alaT | tRNA‑Ala |
| * | NC_000913 | 3,581,773 | 0 | G→A | 100.0% | 1.1 | 2 | intergenic (+147/‑90) | yhhY/yhhZ | aminoacyl nucleotide detoxifying acetyltransferase/putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity |
| * | NC_000913 | 1,633,341 | 0 | T→G | 100.0% | 0.9 | 1 | intergenic (+36/‑281) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 237,256 | 0 | T→G | 100.0% | 0.7 | 1 | intergenic (+249/‑79) | aspV/yafT | tRNA‑Asp/lipoprotein |
| * | NC_000913 | 1,197,769 | 0 | A→C | 100.0% | 0.7 | 1 | F157V (TTT→GTT) | ymfE | e14 prophage; putative inner membrane protein |
| * | NC_000913 | 1,300,674 | 0 | C→A | 100.0% | 0.7 | 1 | intergenic (+1429/‑508) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,300,676 | 0 | C→A | 100.0% | 0.7 | 1 | intergenic (+1431/‑506) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,633,353 | 0 | G→A | 100.0% | 0.7 | 1 | intergenic (+48/‑269) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 1,633,357 | 0 | C→A | 100.0% | 0.7 | 1 | intergenic (+52/‑265) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 1,633,365 | 0 | C→A | 100.0% | 0.7 | 1 | intergenic (+60/‑257) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 1,633,371 | 0 | C→A | 100.0% | 0.7 | 1 | intergenic (+66/‑251) | ydfK/pinQ | cold shock protein, function unknown, Qin prophage/Qin prophage; putative site‑specific recombinase |
| * | NC_000913 | 1,806,265 | 0 | A→C | 100.0% | 0.6 | 1 | intergenic (‑182/‑105) | ydiY/pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| * | NC_000913 | 2,884,293 | 0 | T→A | 100.0% | 0.2 | 2 | intergenic (‑155/+260) | casA/ygcB | CRISP RNA (crRNA) containing Cascade antiviral complex protein/Cascade complex anti‑viral R‑loop helicase‑annealase Cas3 |
| * | NC_000913 | 2,726,597 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2588/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| * | NC_000913 | 2,726,598 | 0 | T→A | 100.0% | ‑0.5 | 1 | noncoding (2587/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| * | NC_000913 | 2,726,602 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2583/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| * | NC_000913 | 2,726,603 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2582/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| * | NC_000913 | 2,726,604 | 0 | C→A | 100.0% | ‑0.5 | 1 | noncoding (2581/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 2,823,830 | 0 | A→G | 24.7% | 50.6 ‑0.2 ‑0.1 | 85 | intergenic (‑61/+19) | recA/pncC | DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor/nicotinamide‑nucleotide amidohydrolase; NMN amidohydrolase |
| * | NC_000913 | 4,296,060 | 0 | C→T | 22.9% | 64.3 0.0 ‑0.0 | 110 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 20 (0.250) | 18/310 | 4.1 | 58.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2462930 = | 14 (0.170) | intergenic (+284/‑82) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 19 (0.240) | 18/302 | 4.0 | 97.4% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 1 (0.010) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1207790 = | 55 (0.680) | 14 (0.190) | 10/278 | 5.9 | 22.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 50 (0.690) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 12 (0.160) | 10/294 | 6.2 | 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 | = 1207805 | 58 (0.720) | 7 (0.100) | 7/278 | 7.2 | 12.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 49 (0.680) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 6 (0.080) | 5/292 | 8.5 | 100% | coding (687/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619892 = | 0 (0.000) | coding (701/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 112281 = | 90 (1.120) | 5 (0.060) | 4/298 | 9.3 | 5.8% | coding (319/744 nt) | zapD | FtsZ stabilizer |
| ? | NC_000913 | 112312 = | 77 (1.000) | coding (288/744 nt) | zapD | FtsZ stabilizer | |||||
| * | ? | NC_000913 | 18671 = | 89 (1.110) | 4 (0.050) | 4/296 | 9.3 | 4.6% | intergenic (+16/‑44) | nhaA/nhaR | sodium‑proton antiporter/transcriptional activator of nhaA |
| ? | NC_000913 | 18691 = | 82 (1.070) | intergenic (+36/‑24) | nhaA/nhaR | sodium‑proton antiporter/transcriptional activator of nhaA | |||||
| * | ? | NC_000913 | 909017 = | 68 (0.840) | 4 (0.050) | 4/296 | 9.3 | 5.7% | coding (278/1002 nt) | ltaE | L‑allo‑threonine aldolase, PLP‑dependent |
| ? | NC_000913 | 909055 = | 68 (0.880) | coding (240/1002 nt) | ltaE | L‑allo‑threonine aldolase, PLP‑dependent | |||||
| * | ? | NC_000913 | = 3699911 | 101 (1.250) | 4 (0.050) | 4/292 | 9.2 | 4.0% | intergenic (+18/+69) | bcsG/ldrD | DUF3260 family cellulose production inner membrane protein/toxic polypeptide, small |
| ? | NC_000913 | = 3699921 | 98 (1.290) | intergenic (+28/+59) | bcsG/ldrD | DUF3260 family cellulose production inner membrane protein/toxic polypeptide, small | |||||
| * | ? | NC_000913 | = 2713829 | 83 (1.030) | 4 (0.050) | 3/288 | 9.8 | 5.0% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713908 | 76 (1.020) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | = 3858205 | 86 (1.070) | 4 (0.050) | 3/284 | 9.7 | 4.7% | coding (200/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | = 3858228 | 83 (1.130) | coding (177/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | = 2236519 | 81 (1.010) | 3 (0.040) | 3/290 | 9.8 | 4.0% | intergenic (+19/+224) | preA/mglC | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C/methyl‑galactoside transporter subunit |
| ? | NC_000913 | = 2236533 | 68 (0.900) | intergenic (+33/+210) | preA/mglC | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C/methyl‑galactoside transporter subunit | |||||
| * | ? | NC_000913 | = 2291160 | 128 (1.590) | 3 (0.040) | 3/292 | 9.9 | 2.4% | noncoding (8/199 nt) | RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site |
| ? | NC_000913 | = 2291167 | 119 (1.570) | noncoding (15/199 nt) | RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 2423437 = | 177 (2.200) | 3 (0.040) | 3/294 | 9.9 | 1.8% | coding (103/891 nt) | yfcI | transposase_31 family protein |
| ? | NC_000913 | 2423471 = | 162 (2.120) | coding (69/891 nt) | yfcI | transposase_31 family protein | |||||
| * | ? | NC_000913 | 2540366 = | 84 (1.040) | 3 (0.040) | 3/300 | 10.0 | 3.7% | coding (449/1098 nt) | cysA | sulfate/thiosulfate transporter subunit |
| ? | NC_000913 | 2540387 = | 74 (0.950) | coding (428/1098 nt) | cysA | sulfate/thiosulfate transporter subunit | |||||
| * | ? | NC_000913 | 2777562 = | 63 (0.780) | 3 (0.040) | 3/292 | 9.9 | 4.8% | coding (110/330 nt) | ypjF | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system |
| ? | NC_000913 | 2777586 = | 60 (0.790) | coding (134/330 nt) | ypjF | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system | |||||
| * | ? | NC_000913 | 3515982 = | 59 (0.730) | 3 (0.040) | 3/292 | 9.9 | 5.2% | intergenic (‑69/+38) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring |
| ? | NC_000913 | 3516010 = | 53 (0.700) | intergenic (‑97/+10) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring | |||||
| * | ? | NC_000913 | 3989869 = | 80 (0.990) | 3 (0.040) | 3/294 | 9.9 | 3.6% | coding (898/942 nt) | hemC | hydroxymethylbilane synthase |
| ? | NC_000913 | 3989977 = | 87 (1.140) | coding (790/942 nt) | hemC | hydroxymethylbilane synthase | |||||