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 | 18,126 | T→G | 25.2% | V213G (GTG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 123,466 | T→G | 26.3% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 238,497 | G→T | 33.6% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 29.3% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 22.7% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 21.5% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 23.4% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 33.0% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| RA | 252,247 | A→G | 5.3% | E81E (GAA→GAG) | yafN → | antitoxin YafN |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 454,873 | C→G | 56.9% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,877 | A→T | 38.5% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,883 | C→G | 36.4% | intergenic (+94/‑250) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,885 | C→G | 38.3% | intergenic (+96/‑248) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,926 | G→T | 57.5% | intergenic (+137/‑207) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 495,537 | C→A | 5.2% | R140S (CGT→AGT) | htpG → | chaperone protein HtpG |
| RA | 569,270 | C→T | 7.0% | D123D (GAC→GAT) | ybcK → | DLP12 prophage; putative recombinase |
| RA | 642,840 | A→C | 14.2% | Q251H (CAA→CAC) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 736,663 | C→T | 5.4% | T73T (ACC→ACT) | ybfQ → | inactive transposase YbfQ |
| RA | 815,874 | C→T | 6.7% | G258G (GGG→GGA) | ybhK ← | putative transferase YbhK |
| RA | 896,486 | A→G | 7.0% | Y118C (TAT→TGT) | potH → | putrescine ABC transporter membrane subunit PotH |
| RA | 901,699 | C→T | 9.0% | V184V (GTG→GTA) | artQ ← | L‑arginine ABC transporter membrane subunit ArtQ |
| MC JC | 932,613 | Δ459 bp | 100% | coding (19‑477/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,186,776 | T→C | 9.8% | I311I (ATT→ATC) | pepT → | peptidase T |
| RA | 1,254,034 | T→G | 15.2% | N640T (AAC→ACC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,295,520 | C→A | 21.6% | V868L (GTA→TTA) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,332,759 | T→A | 10.1% | F571Y (TTC→TAC) | topA → | DNA topoisomerase 1 |
| JC | 1,333,434 | Δ69 bp | 39.0% | coding (2387‑2455/2598 nt) | topA → | DNA topoisomerase 1 |
| RA | 1,350,490 | C→T | 5.1% | V184I (GTT→ATT) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase |
| RA | 1,511,235 | C→T | 7.4% | A411A (GCC→GCT) | ydcR → | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YdcR |
| RA | 1,578,744 | A→C | 12.6% | L200R (CTC→CGC) | yddA ← | ABC transporter family protein YddA |
| RA | 1,617,335 | T→G | 16.5% | V103G (GTT→GGT) | ydeA → | L‑arabinose exporter |
| RA | 1,850,759 | C→T | 5.9% | intergenic (+66/‑101) | sppA → / → ansA | protease IV, a signal peptide peptidase/L‑asparaginase 1 |
| RA | 1,885,279 | C→T | 7.5% | N205N (AAC→AAT) | yeaW → | carnitine monooxygenase subunit YeaW |
| RA | 1,906,237 | A→C | 33.4% | T184P (ACG→CCG) | mntP → | Mn(2(+)) exporter |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,078,318 | C→A | 14.6% | intergenic (+184/‑257) | yeeW → / → yoeF | CP4‑44 prophage; putative uncharacterized protein YeeW/CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,115,570 | G→A | 5.5% | G109G (GGC→GGT) | wcaM ← | putative colanic acid biosynthesis protein WcaM |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,176,251 | G→A | 6.1% | P24L (CCG→CTG) | gatZ ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatZ |
| RA | 2,177,234 | C→A | 41.4% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 55.1% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,265,423 | G→T | 13.4% | intergenic (‑128/‑27) | yeiW ← / → yeiP | PF03692 putative metal‑chelating domain‑containing protein YeiW/elongation factor P family protein |
| RA | 2,470,431 | G→T | 43.5% | R434I (AGA→ATA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,435 | T→A | 25.6% | N435K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,439 | G→C | 30.4% | D437H (GAC→CAC) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,444 | T→A | 25.9% | N438K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,871,848 | T→G | 15.1% | T215P (ACG→CCG) | ispD ← | 2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 2,900,711 | G→T | 15.3% | M40I (ATG→ATT) | yqcE → | putative transport protein YqcE |
| RA | 2,975,236 | A→G | 5.6% | L260S (TTA→TCA) | aas ← | acyltransferase |
| RA | 3,021,081 | C→A | 12.3% | A181E (GCA→GAA) | ygfM → | putative oxidoreductase |
| JC JC | 3,117,469 | IS4 (+) +13 bp | 18.7% | coding (1632‑1644/4563 nt) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,171,103 | T→A | 18.2% | L207Q (CTA→CAA) | qseC → | sensory histidine kinase QseC |
| RA | 3,229,231 | T→A | 7.4% | I115N (ATT→AAT) | ygjK → | glycoside hydrolase |
| RA | 3,246,808 | A→T | 5.2% | I53F (ATC→TTC) | exuR → | DNA‑binding transcriptional repressor ExuR |
| RA | 3,406,992 | C→A | 6.0% | A359E (GCA→GAA) | accC → | biotin carboxylase |
| RA | 3,418,500 | T→A | 23.4% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,482,567 | G→C | 23.3% | E427Q (GAA→CAA) | yheS → | ABC transporter ATP‑binding protein YheS |
| RA | 3,559,250 | C→T | 5.7% | A328V (GCC→GTC) | rtcR → | DNA‑binding transcriptional activator RtcR |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,572,062 | A→G | 8.0% | W481R (TGG→CGG) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,595,172 | Δ1 bp | 6.7% | coding (309/1278 nt) | livM ← | branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM |
| RA | 3,602,318 | G→C | 5.4% | Q144E (CAG→GAG) | ftsE ← | cell division protein FtsE |
| RA | 3,654,699 | C→A | 16.7% | T6N (ACC→AAC) | dctR → | putative DNA‑binding transcriptional regulator DctR |
| RA | 3,676,687 | G→A | 5.4% | A555V (GCG→GTG) | yhjG ← | AsmA family protein YhjG |
| RA | 3,756,565 | C→A | 22.1% | intergenic (‑54/+111) | aldB ← / ← yiaY | aldehyde dehydrogenase B/L‑threonine dehydrogenase |
| RA | 3,828,980 | A→C | 24.6% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,828,985 | T→G | 51.6% | V14G (GTT→GGT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 4,006,913 | T→G | 22.5% | R350R (CGT→CGG) | recQ → | ATP‑dependent DNA helicase RecQ |
| RA | 4,051,505 | A→G | 7.4% | S53S (TCA→TCG) | yihI → | Der GTPase‑activating protein YihI |
| RA | 4,054,663 | C→T | 5.7% | E206K (GAA→AAA) | glnG ← | DNA‑binding transcriptional dual regulator NtrC |
| RA | 4,182,820 | C→T | 61.0% | H526Y (CAC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,283,228 | T→G | 56.7% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 28.0% | 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 | 4,470,237 | Δ1 bp | 7.5% | coding (2613/2697 nt) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,470,238 | Δ1 bp | 7.5% | coding (2614/2697 nt) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,470,239 | Δ1 bp | 7.5% | coding (2615/2697 nt) | mgtA → | Mg(2(+)) importing P‑type ATPase |
| RA | 4,606,205 | C→G | 38.5% | noncoding (82/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,207 | A→C | 41.7% | noncoding (80/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,613,308 | A→C | 30.8% | T300P (ACG→CCG) | yjjU → | putative patatin‑like phospholipase YjjU |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423759–3424234 | 3424546–3424238 | 5–788 | 22 [21] | [21] 24 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 30 (0.430) | 46 (0.770) | 34/204 | NT | 68.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 17 (0.280) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.430) | 18 (0.300) | 11/204 | NT | 45.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 17 (0.280) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 93 (1.390) | 48/228 | 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 | |||||
| * | ? | NC_000913 | 2941850 = | 54 (0.780) | 13 (0.190) | 10/232 | NT | 16.0% | coding (718/918 nt) | gcvA | DNA‑binding transcriptional dual regulator GcvA |
| ? | NC_000913 | = 3135389 | 83 (1.220) | coding (983/1500 nt) | pitB | metal phosphate:H(+) symporter PitB | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 21 (0.300) | 18/236 | NT | 26.9% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3877530 | 57 (0.820) | intergenic (‑65/+175) | yidB/gyrB | conserved protein YidB/DNA gyrase subunit B | |||||