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 |
| Marginal read alignment evidence (highest frequency 20 of 281 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 44.4% | 91.0 / 21.5 | 72 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 43.9% | 53.0 / 28.1 | 68 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 42.4% | 161.4 / 64.8 | 118 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 2,331,202 | 0 | A | C | 39.2% | 132.2 / 18.6 | 77 | G566G (GGT→GGG) | gyrA | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| * | NZ_CP009273 | 1,155,293 | 0 | A | G | 37.4% | 128.1 / 28.0 | 83 | I572T (ATC→ACC) | fhuE | ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE |
| * | NZ_CP009273 | 2,221,754 | 0 | T | C | 37.0% | 72.0 / 14.0 | 55 | pseudogene (484/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NZ_CP009273 | 2,428,361 | 0 | T | G | 36.9% | 109.0 / 17.9 | 65 | Y252S (TAC→TCC) | truA | tRNA pseudouridine(38‑40) synthase TruA |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 35.3% | 106.9 / 42.0 | 69 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 4,151,076 | 0 | G | A | 35.0% | 159.2 / 44.0 | 97 | E10K (GAA→AAA) | fabR | HTH‑type transcriptional repressor FabR |
| * | NZ_CP009273 | 3,806,632 | 0 | C | T | 34.4% | 129.6 / 35.9 | 90 | S181L (TCG→TTG) | coaBC | bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC |
| * | NZ_CP009273 | 2,897,051 | 0 | C | A | 34.3% | 198.8 / 51.4 | 99 | intergenic (+318/+1055) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 2,089,571 | 0 | A | G | 34.2% | 143.7 / 26.6 | 82 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase subunit HisF |
| * | NZ_CP009273 | 3,344,212 | 0 | A | C | 34.0% | 215.0 / 11.7 | 94 | S725A (TCA→GCA) | arcB | aerobic respiration two‑component sensor histidine kinase ArcB |
| * | NZ_CP009273 | 1,995,399 | 0 | A | C | 33.8% | 157.8 / 13.0 | 78 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NZ_CP009273 | 1,560,495 | 0 | C | T | 33.3% | 129.1 / 16.8 | 72 | T301T (ACG→ACA) | dosC | diguanylate cyclase DosC |
| * | NZ_CP009273 | 2,372,447 | 0 | C | T | 33.3% | 63.8 / 16.4 | 55 | E98K (GAA→AAA) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase |
| * | NZ_CP009273 | 2,840,033 | 0 | T | G | 33.3% | 132.1 / 20.1 | 77 | T247P (ACC→CCC) | hycD | formate hydrogenlyase subunit HycD |
| * | NZ_CP009273 | 2,845,013 | 0 | T | G | 33.3% | 144.4 / 18.2 | 77 | G218G (GGT→GGG) | hypB | hydrogenase nickel incorporation protein HypB |
| * | NZ_CP009273 | 2,738,448 | 0 | A | C | 33.0% | 218.7 / 23.4 | 105 | V84G (GTG→GGG) | trmD | tRNA (guanosine(37)‑N1)‑methyltransferase TrmD |
| * | NZ_CP009273 | 429,105 | 0 | T | G | 32.6% | 104.2 / 15.2 | 92 | G65G (GGT→GGG) | ribD | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase RibD |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | 45 (0.430) | 53 (0.510) | 47/496 | 3.0 | 47.8% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 71 (0.680) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | = 3416707 | 94 (0.900) | 6 (0.250) +191 bp |
6/114 | 3.3 | 22.3% | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 3416716 = | 90 (0.860) | intergenic (+163/+68) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 50 (0.480) | 42 (0.410) +AATTCC |
37/484 | 4.3 | 36.6% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 99 (0.950) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 62 (0.590) | 8 (0.120) +93 bp |
7/310 | 9.7 | 14.1% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416707 | 94 (0.900) | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 360286 | 71 (0.680) | 16 (0.160) +AATTC |
15/486 | 10.1 | 19.7% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 62 (0.590) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 120 (1.150) | 10 (0.100) | 10/478 | 12.2 | 8.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 104 (1.030) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 62 (0.590) | 9 (0.090) +GAATTAATTCC |
8/474 | 13.2 | 10.5% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 4161677 = | 99 (0.950) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 4532499 = | 116 (1.110) | 7 (0.070) | 7/478 | 13.8 | 6.1% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 104 (1.030) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 360104 = | 50 (0.480) | 5 (0.050) +AATTCC |
5/484 | 15.3 | 6.6% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 94 (0.900) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3731803 = | 118 (1.130) | 3 (0.030) | 3/492 | 17.0 | 2.5% | coding (947/2031 nt) | malS | alpha‑amylase |
| ? | NZ_CP009273 | 3731833 = | 118 (1.140) | coding (977/2031 nt) | malS | alpha‑amylase | |||||