mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 70,434 | C→T | 41.9% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 54.3% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 39.9% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 51.9% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 54.6% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 52.1% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 55.1% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 61.1% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 57.7% | F276F (TTT→TTC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 153,700 | A→G | 5.9% | L576P (CTT→CCT) | htrE ← | predicted outer membrane usher protein |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 236,101 | A→C | 52.5% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 49.0% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 547,694 | A→G | 100% | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,831:1 | +G | 100% | pseudogene (251/261 nt) pseudogene (251/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 671,132 | C→T | 9.7% | R299H (CGT→CAT) | holA ← | DNA polymerase III, delta subunit |
| RA | 711,258 | T→A | 11.7% | intergenic (‑190/+99) | fur ← / ← fldA | DNA‑binding transcriptional dual regulator/flavodoxin 1 |
| RA | 711,262 | A→C | 11.3% | intergenic (‑194/+95) | fur ← / ← fldA | DNA‑binding transcriptional dual regulator/flavodoxin 1 |
| RA | 711,264 | A→C | 10.7% | intergenic (‑196/+93) | fur ← / ← fldA | DNA‑binding transcriptional dual regulator/flavodoxin 1 |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| MC JC | 1,301,041 | Δ1,336 bp | 100% | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,490,052 | C→T | 6.7% | S36F (TCC→TTC) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,733,486 | C→A | 19.0% | L896M (CTG→ATG) | lhr → | predicted ATP‑dependent helicase |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,461,546:1 | +A | 8.3% | intergenic (‑454/+227) | yfcV ← / ← sixA | predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| RA | 2,461,548 | G→T | 8.6% | intergenic (‑456/+225) | yfcV ← / ← sixA | predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| RA | 2,461,557 | A→C | 8.9% | intergenic (‑465/+216) | yfcV ← / ← sixA | predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| RA | 2,461,559 | Δ1 bp | 7.6% | intergenic (‑467/+214) | yfcV ← / ← sixA | predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| RA | 2,809,581 | G→A | 65.1% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 2,899,219 | T→C | 6.4% | intergenic (‑290/‑29) | ygcW ← / → yqcE | predicted deoxygluconate dehydrogenase/predicted transporter |
| RA | 3,227,650 | G→C | 22.3% | G36A (GGC→GCC) ‡ | ygjK → | predicted glycosyl hydrolase |
| RA | 3,227,651 | C→G | 21.1% | G36G (GGC→GGG) ‡ | ygjK → | predicted glycosyl hydrolase |
| RA | 3,227,656 | C→G | 21.1% | P38R (CCG→CGG) ‡ | ygjK → | predicted glycosyl hydrolase |
| RA | 3,227,657 | G→C | 21.1% | P38P (CCG→CCC) ‡ | ygjK → | predicted glycosyl hydrolase |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| MC JC | 3,742,938 | Δ1,336 bp | 100% | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | 100% | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| RA | 3,824,280 | T→C | 100% | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | 100% | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | 100% | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | 100% | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | 100% | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | 100% | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | 100% | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | 100% | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | 100% | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,533:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,637,896 | G→T | 7.1% | intergenic (+128/+19) | trpR → / ← yjjX | DNA‑binding transcriptional repressor, tryptophan‑binding/thiamin metabolism associated protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 171676 | 171700 | 25 | 10 [2] | [4] 10 | fhuB | fused subunits of iron‑hydroxamate transporter and membrane components of ABC superfamily transporter |
| * | * | ÷ | W3110S.gb | 422773 | 422787 | 15 | 8 [3] | [0] 10 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573863–575008 | 575999 | 992–2137 | 7 [3] | [0] 176 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 721522 | 721545 | 24 | 7 [4] | [5] 11 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 1081332 | 1081358 | 27 | 7 [4] | [1] 8 | putP/ycdN | proline:sodium symporter/ECK1007:JW5141:b1016; hypothetical protein, N‑ter fragment |
| * | * | ÷ | W3110S.gb | 1352906 | 1352938–1352923 | 18–33 | 6 [3] | [5] 8 | fabI/ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 2041775 | 2041789 | 15 | 9 [1] | [0] 7 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2296359 | 2296406 | 48 | 11 [5] | [5] 11 | ccmF | heme lyase, CcmF subunit |
| * | * | ÷ | W3110S.gb | 2569102 | 2569128 | 27 | 8 [4] | [5] 11 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2777815 | 2777840 | 26 | 6 [5] | [0] 13 | ypjA | adhesin‑like autotransporter |
| * | * | ÷ | W3110S.gb | 2827399 | 2827434 | 36 | 6 [0] | [4] 7 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 3859259 | 3859264 | 6 | 12 [5] | [0] 7 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 4213636–4215889 | 4216704–4215891 | 3–3069 | 9 [5] | [5] 7 | [rrlE]–[rrfE] | [rrlE],[rrfE] |
| * | * | ÷ | W3110S.gb | 4329957 | 4329989 | 33 | 6 [4] | [4] 6 | [phnB] | [phnB] |
| * | * | ÷ | W3110S.gb | 4401118 | 4401187 | 70 | 10 [4] | [3] 6 | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 70061 = | 29 (0.500) | 58 (1.280) +CGCGTACAACT |
20/78 | NT | 54.3% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 97 (1.660) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 44 (0.750) | 48 (1.150) +AGGGTCCCTAAGTC |
18/72 | NT | 66.4% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 24 (0.410) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 236798 | 43 (0.740) | 35 (1.330) +27 bp |
18/46 | NT | 63.7% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 46 (0.790) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 70 (1.200) | 16/100 | NT | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 41 (0.700) | 93 (1.660) +TC |
24/96 | NT | 82.5% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 97 (1.660) | 24/100 | NT | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 52 (0.890) | 17/100 | NT | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 713380 = | 32 (0.550) | 48 (0.890) | 19/92 | NT | 59.9% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 35 (0.650) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 87 (1.490) | 87 (1.490) | 21/100 | NT | 47.2% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 108 (1.850) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 11 (0.190) | 25 (0.640) | 11/68 | NT | 56.6% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 31 (0.790) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 17 (0.290) | 19 (0.480) | 6/68 | NT | 47.2% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 31 (0.790) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 6 (0.100) | 70 (1.280) | 19/94 | NT | 92.6% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 0 (0.000) | 34 (0.610) | 11/96 | NT | 100% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | 2172308 = | NA (NA) | 103 (1.800) | 24/98 | NT | 100% | pseudogene (1563/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 91 (1.590) | 21/98 | NT | 100% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 0 (0.000) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173565 | NA (NA) | 20 (0.340) | 10/100 | NT | 100% | pseudogene (306/2041 nt) pseudogene (306/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | = 3932933 | 0 (0.000) | coding (222/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 77 (1.320) | 20/100 | NT | 88.5% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 10 (0.170) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 3748799 = | 4 (0.070) | 90 (1.540) | 26/100 | NT | 95.7% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | = 3750592 | 0 (0.000) | 131 (2.440) | 32/92 | NT | 100% | intergenic (‑104/‑69) | tnaA/insH | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/IS5 element protein |
| ? | W3110S.gb | 3751792 = | 0 (0.000) | intergenic (+151/+116) | insH/tnaC | IS5 element protein/tryptophanase leader peptide | |||||
| * | ? | W3110S.gb | 4547364 = | 49 (0.840) | 22 (0.460) | 7/82 | NT | 37.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 35 (0.730) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 41 (0.700) | 7 (0.150) | 5/82 | NT | 17.0% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 35 (0.730) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||