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 | 31,745 | T→G | 5.1% | L310R (CTG→CGG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 68,486 | T→G | 11.1% | L217V (TTG→GTG) | yabI → | DedA family inner membrane protein |
| RA | 148,175 | C→G | 5.7% | V182L (GTA→CTA) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 148,214 | G→T | 6.1% | P169T (CCG→ACG) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 161,068 | A→C | 30.0% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 169,946 | G→C | 5.0% | intergenic (+15/+143) | fhuB → / ← hemL | fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components/glutamate‑1‑semialdehyde aminotransferase (aminomutase) |
| RA | 221,380 | T→A | 5.1% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 5.4% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 5.4% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 6.0% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 6.0% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 6.0% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 6.0% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 5.8% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 6.2% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 6.7% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 6.9% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 6.8% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 7.1% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 7.1% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 6.9% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,471 | C→T | 6.5% | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,476 | A→T | 7.2% | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 235,019 | C→A | 6.3% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 277,676 | A→C | 10.2% | W7G (TGG→GGG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 328,921 | T→G | 6.5% | D280E (GAT→GAG) | yahA → | c‑di‑GMP‑specific phosphodiesterase |
| RA | 357,048 | G→C | 7.5% | A175G (GCT→GGT) | lacA ← | thiogalactoside acetyltransferase |
| RA | 418,995 | T→G | 12.6% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 445,212 | C→T | 100% | G296S (GGT→AGT) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 503,882 | G→T | 8.4% | W70L (TGG→TTG) | ybaQ → | putative DNA‑binding transcriptional regulator |
| RA | 503,903 | T→G | 6.1% | V77G (GTT→GGT) | ybaQ → | putative DNA‑binding transcriptional regulator |
| RA | 513,790 | T→G | 8.1% | intergenic (‑55/+6) | ybbN ← / ← ybbO | DnaK co‑chaperone, thioredoxin‑like protein/putative oxidoreductase |
| RA | 620,054 | A→T | 15.9% | intergenic (‑88/‑287) | fepB ← / → entC | iron‑enterobactin transporter subunit/isochorismate synthase 1 |
| RA | 763,357 | A→T | 6.6% | M640L (ATG→TTG) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 763,400 | A→T | 5.4% | D654V (GAT→GTT) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 777,128 | A→C | 5.3% | intergenic (+20/‑413) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 838,707 | A→C | 5.3% | Q307P (CAG→CCG) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 910,671 | T→G | 6.6% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 910,682 | T→G | 11.7% | intergenic (‑369/+126) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 1,288,276 | C→A | 100% | V35F (GTT→TTT) | hns ← | global DNA‑binding transcriptional dual regulator H‑NS |
| RA | 1,345,477 | T→A | 5.3% | intergenic (‑181/+187) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,630,709 | C→G | 8.1% | intergenic (‑85/‑304) | nohQ ← / → ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| RA | 1,672,825 | G→T | 11.9% | A48S (GCT→TCT) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,683,030 | A→C | 5.3% | K66N (AAA→AAC) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,828,727 | G→C | 14.7% | E119Q (GAA→CAA) ‡ | ydjY → | putative ferrodoxin‑like lipoprotein |
| RA | 1,828,729 | A→C | 9.5% | E119D (GAA→GAC) ‡ | ydjY → | putative ferrodoxin‑like lipoprotein |
| RA | 2,170,707 | C→A | 9.6% | intergenic (‑24/+284) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,713 | C→A | 14.9% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,724 | G→T | 17.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,746 | C→A | 16.7% | intergenic (‑63/+245) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,754 | C→A | 10.3% | intergenic (‑71/+237) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,758 | C→A | 11.6% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,222,656 | A→C | 12.1% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,463,910 | G→T | 23.4% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,463,915 | C→A | 25.6% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,475,229 | C→A | 6.4% | A143S (GCT→TCT) | emrY ← | putative multidrug efflux system |
| RA | 2,632,621 | T→G | 12.0% | N8H (AAC→CAC) | yfgM ← | putative anti‑RcsB factor |
| RA | 2,632,626 | T→G | 6.7% | N6T (AAC→ACC) | yfgM ← | putative anti‑RcsB factor |
| RA | 2,711,677 | T→G | 8.5% | T71P (ACG→CCG) | yfiF ← | putative methyltransferase |
| RA | 2,719,149 | T→G | 11.0% | intergenic (‑44/+279) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,861,083 | G→T | 5.7% | Q344K (CAA→AAA) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 3,039,409 | T→G | 6.4% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| RA | 3,048,261 | C→G | 6.2% | P181P (CCG→CCC) | ygfB ← | UPF0149 family protein |
| RA | 3,072,806 | A→G | 100% | intergenic (‑117/+197) | cmtB ← / ← tktA | putative mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamine triphosphate‑binding |
| RA | 3,384,766 | A→C | 6.1% | F208V (TTT→GTT) | tldD ← | putative peptidase |
| RA | 3,385,479 | C→G | 5.9% | intergenic (‑92/+338) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,449,050 | C→A | 14.7% | F38L (TTC→TTA) | gspC → | general secretory pathway component, cryptic |
| RA | 3,498,220 | T→G | 11.8% | intergenic (+78/+74) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,525,235 | C→A | 5.0% | T188T (ACG→ACT) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,546,300 | G→T | 5.2% | intergenic (‑468/‑144) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| RA | 3,602,075 | A→C | 8.5% | intergenic (+66/+36) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,774,404 | T→A | 5.4% | intergenic (+27/‑171) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,822,340 | A→C | 9.6% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,901,867 | T→G | 7.4% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,991,416 | T→G | 9.1% | L25R (CTT→CGT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 3,997,357 | G→C | 6.3% | S61C (TCC→TGC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,066,050 | G→T | 5.8% | A294A (GCC→GCA) | yihU ← | gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent |
| RA | 4,171,201 | G→C | 69.8% | R10P (CGT→CCT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,178,500 | C→T | 24.4% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,234,521 | T→G | 5.6% | E161D (GAA→GAC) | malF ← | maltose transporter subunit |
| RA | 4,234,533 | C→G | 7.3% | L157L (CTG→CTC) | malF ← | maltose transporter subunit |
| RA | 4,236,457 | T→G | 9.4% | intergenic (‑110/‑255) | malE ← / → malK | maltose transporter subunit/fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein |
| RA | 4,286,083 | T→C | 5.2% | intergenic (+361/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,286,118 | A→G | 6.8% | intergenic (+396/+135) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,286,119 | A→C | 9.1% | intergenic (+397/+134) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,375,498 | G→T | 9.1% | E97* (GAA→TAA) | yjeN → | uncharacterized protein |
| RA | 4,467,839 | A→C | 6.4% | L97R (CTT→CGT) | argI ← | ornithine carbamoyltransferase 1 |
| RA | 4,561,269 | G→A | 100% | S41S (AGC→AGT) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 4323048 | 4323809 | 762 | 188 [186] | [185] 188 | [basS]–[eptA] | [basS],basR,[eptA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 448 (0.890) | 480 (0.950) | 85/250 | NT | 51.7% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 776010 = | 525 (1.040) | 106 (0.210) +G |
7/248 | NT | 18.7% | noncoding (1/76 nt) | lysT | tRNA‑Lys |
| ? | CP009273 | = 2514488 | 402 (0.800) | noncoding (216/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | 1203246 = | 263 (0.520) | 273 (0.620) | 70/218 | NT | 57.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 176 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 256 (0.510) | 316 (0.720) | 62/218 | NT | 61.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 176 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 4532507 | 130 (0.260) | 16 (0.030) | 12/232 | NT | 7.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 290 (0.620) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||