mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 18,124 | C→G | 34.2% | G212G (GGC→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 18,126 | T→G | 27.5% | V213G (GTG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 18,141 | C→G | 27.5% | A218G (GCG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 99,074 | C→T | 6.1% | A224A (GCC→GCT) | ftsW → | putative lipid II flippase FtsW |
| RA | 103,666 | T→C | 5.7% | L171S (TTG→TCG) | ftsQ → | cell division protein FtsQ |
| RA | 123,466 | T→G | 23.2% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 175,235 | C→T | 6.0% | G43G (GGC→GGT) | clcA → | chloride:H(+) antiporter ClcA |
| RA | 176,987 | C→A | 32.7% | intergenic (+33/+14) | erpA → / ← yadS | iron‑sulfur cluster insertion protein ErpA/conserved inner membrane protein YadS |
| RA | 238,497 | G→T | 18.3% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 21.4% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 18.9% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 24.6% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 28.6% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 261,581 | G→A | 6.4% | V27M (GTG→ATG) | proA → | glutamate‑5‑semialdehyde dehydrogenase |
| RA | 285,813 | A→G | 5.0% | K140R (AAA→AGA) | yagG → | putative D‑xylonate transporter YagG |
| RA | 290,142 | T→G | 11.6% | D55A (GAC→GCC) | argF ← | CP4‑6 prophage; ornithine carbamoyltransferase ArgF |
| RA | 362,994 | C→T | 6.2% | L62L (CTG→CTA) | lacY ← | lactose permease |
| RA | 389,306 | T→G | 23.6% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | 454,877 | A→T | 32.8% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,883 | C→G | 28.1% | intergenic (+94/‑250) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 458,435 | A→C | 7.2% | Y337S (TAT→TCT) | clpX → | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 465,604 | C→T | 5.5% | intergenic (‑57/+8) | queC ← / ← ybaE | 7‑cyano‑7‑deazaguanine synthase/putative protein YbaE |
| RA | 729,383 | T→G | 30.3% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 750,213 | G→T | 6.5% | R653S (CGC→AGC) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 840,774 | T→A | 21.0% | Y253F (TAT→TTT) | fiu ← | putative iron siderophore outer membrane transporter |
| RA | 936,119 | G→A | 7.3% | V966M (GTG→ATG) | ftsK → | cell division DNA translocase FtsK |
| RA | 1,037,224 | C→T | 5.9% | P159L (CCG→CTG) | hyaF → | protein HyaF |
| RA | 1,097,634 | G→C | 6.1% | noncoding (19/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,124,075 | T→C | 6.3% | intergenic (‑21/+43) | grxB ← / ← mdtH | reduced glutaredoxin 2/multidrug efflux pump MdtH |
| JC JC | 1,222,909 | IS2 (–) +5 bp | 15.6% | coding (76‑80/345 nt) | ymgG ← | PF13488 family protein YmgG |
| RA | 1,229,755 | T→C | 6.9% | K214E (AAG→GAG) | hlyE ← | hemolysin E |
| RA | 1,328,099 | T→A | 7.3% | M87L (ATG→TTG) | btuR ← | cobinamide/cobalamin adenosyltransferase |
| RA | 1,446,656 | G→T | 20.2% | R210S (CGC→AGC) | feaR ← | DNA‑binding transcriptional activator FeaR |
| RA | 1,664,414 | T→G | 17.1% | V269G (GTG→GGG) | ynfH → | putative menaquinol dehydrogenase |
| RA | 1,693,416 | A→C | 26.9% | L283R (CTG→CGG) | uidB ← | glucuronide:H(+) symporter |
| RA | 1,716,784 | A→T | 5.7% | S147T (TCC→ACC) | tyrS ← | tyrosine‑‑tRNA ligase |
| RA | 1,740,661 | T→C | 5.1% | F251L (TTT→CTT) | ydhC → | putative transporter YdhC |
| RA | 1,779,503 | G→A | 5.1% | intergenic (‑202/‑114) | ydiP ← / → ydiQ | putative DNA‑binding transcriptional regulator YdiP/putative electron transfer flavoprotein subunit YdiQ |
| RA | 1,797,323 | C→T | 8.5% | E208K (GAA→AAA) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,809,670 | Δ1 bp | 6.0% | coding (291/669 nt) | hxpB → | hexitol phosphatase B |
| RA | 1,809,671 | Δ1 bp | 6.0% | coding (292/669 nt) | hxpB → | hexitol phosphatase B |
| RA | 1,860,125 | G→C | 33.9% | V35V (GTC→GTG) | ydjK ← | putative transporter YdjK |
| RA | 1,906,237 | A→C | 34.2% | T184P (ACG→CCG) | mntP → | Mn(2(+)) exporter |
| RA | 1,975,796 | C→A | 5.5% | D154Y (GAT→TAT) | motB ← | motility protein B |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,026,329 | G→A | 6.3% | N563N (AAC→AAT) | dgcQ ← | putative diguanylate cyclase DgcQ |
| RA | 2,130,400 | A→G | 7.0% | L160P (CTG→CCG) | wcaD ← | putative colanic acid polymerase |
| RA | 2,139,598 | T→G | 45.0% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,288,515 | A→C | 16.7% | pseudogene (400/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,470,427 | C→A | 41.2% | Q433K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,436 | C→A | 25.2% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,441 | C→A | 30.5% | D437E (GAC→GAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,735,670 | C→T | 5.1% | T114T (ACG→ACA) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase |
| RA | 2,941,610 | T→A | 7.2% | I8F (ATT→TTT) | ygdD ← | conserved inner membrane protein YgdD |
| RA | 2,942,564 | A→T | 5.4% | S2T (TCT→ACT) | gcvA ← | DNA‑binding transcriptional dual regulator GcvA |
| RA | 2,966,162 | G→A | 6.4% | intergenic (‑125/+26) | lgt ← / ← ptsP | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase/phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,040,491 | C→T | 5.6% | L111L (CTG→CTA) | ygfX ← | protein YgfX |
| RA | 3,135,899 | G→A | 6.1% | S158L (TCG→TTG) | pitB ← | metal phosphate:H(+) symporter PitB |
| RA | 3,212,332 | T→A | 6.8% | I409K (ATA→AAA) | dnaG → | DNA primase |
| RA | 3,378,551 | C→T | 6.8% | R34H (CGT→CAT) | rplM ← | 50S ribosomal subunit protein L13 |
| MC JC | 3,384,721 | Δ435 bp | 100% | coding (19‑453/471 nt) | argR → | DNA‑binding transcriptional dual regulator ArgR |
| RA | 3,454,069 | G→T | 25.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,529,486 | A→G | 6.1% | K47E (AAA→GAA) | hslR → | heat shock protein Hsp15 |
| RA | 3,554,292 | A→G | 13.3% | D403G (GAC→GGC) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,815,809 | Δ1 bp | 100% | intergenic (‑41/+54) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| RA | 3,828,980 | A→C | 37.5% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,838,958 | G→A | 6.3% | L237L (CTG→CTA) | yicL → | putative inner membrane protein |
| RA | 3,934,117 | G→T | 24.7% | D114Y (GAC→TAC) | rbsA → | ribose ABC transporter ATP binding subunit |
| RA | 4,031,912 | A→G | 5.5% | Y251C (TAT→TGT) | pepQ → | Xaa‑Pro dipeptidase |
| RA | 4,099,278 | G→C | 6.0% | Q211H (CAG→CAC) | rhaR → | DNA‑binding transcriptional activator RhaR |
| RA | 4,147,709 | C→G | 12.8% | S203S (TCG→TCC) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| RA | 4,183,258 | G→A | 100% | E672K (GAA→AAA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,220,018 | G→T | 25.5% | D475Y (GAT→TAT) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,296,060 | C→T | 27.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,309,975 | C→T | 7.7% | V336M (GTG→ATG) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,432,278 | G→A | 5.6% | P260L (CCG→CTG) | ytfF ← | inner membrane protein YtfF |
| RA | 4,531,231 | T→A | 16.3% | I141F (ATT→TTT) | sgcX ← | KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain |
| RA | 4,591,815 | G→C | 5.3% | L53L (CTG→CTC) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| RA | 4,640,379 | C→T | 6.3% | intergenic (‑73/‑23) | arcA ← / → yjjY | DNA‑binding transcriptional dual regulator ArcA/protein YjjY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423759–3424234 | 3424534–3424238 | 5–776 | 23 [20] | [20] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 18 (0.280) | 53 (0.950) | 35/202 | NT | 68.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 33 (0.590) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 18 (0.280) | 18 (0.320) | 13/202 | NT | 42.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 33 (0.590) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 80 (1.280) | 47/226 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||