mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 418 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,995,399 | 0 | A | C | 44.1% | 165.2 / 18.7 | 94 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NZ_CP009273 | 3,856,021 | 0 | T | G | 42.5% | 20.9 / 15.6 | 48 | pseudogene (943/1617 nt) | BW25113_RS19145 | PTS sugar transporter subunit IIB |
| * | NZ_CP009273 | 3,856,028 | 0 | A | G | 42.3% | 42.3 / 14.1 | 52 | pseudogene (936/1617 nt) | BW25113_RS19145 | PTS sugar transporter subunit IIB |
| * | NZ_CP009273 | 2,319,929 | 0 | T | G | 41.5% | 118.4 / 43.4 | 82 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NZ_CP009273 | 748,581 | 0 | T | A | 41.4% | 151.0 / 48.9 | 99 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 41.3% | 82.2 / 13.5 | 46 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 894,054 | 0 | T | A | 40.0% | 81.2 / 23.5 | 55 | A27A (GCT→GCA) | rlmC | 23S rRNA (uracil(747)‑C(5))‑methyltransferase RlmC |
| * | NZ_CP009273 | 2,331,202 | 0 | A | C | 40.0% | 134.6 / 31.2 | 80 | G566G (GGT→GGG) | gyrA | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 40.0% | 44.8 / 12.1 | 50 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 1,995,392 | 0 | G | A | 39.8% | 129.6 / 41.8 | 94 | intergenic (‑122/+199) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NZ_CP009273 | 1,570,334 | 0 | C | A | 39.7% | 147.5 / 28.6 | 79 | D515Y (GAT→TAT) | yddB | TonB‑dependent receptor plug domain‑containing protein |
| * | NZ_CP009273 | 3,856,024 | 0 | C | G | 39.6% | 15.4 / 19.7 | 49 | pseudogene (940/1617 nt) | BW25113_RS19145 | PTS sugar transporter subunit IIB |
| * | NZ_CP009273 | 2,658,255 | 0 | T | G | 39.6% | 170.4 / 17.4 | 91 | G169G (GGT→GGG) | yfhR | alpha/beta hydrolase |
| * | NZ_CP009273 | 341,039 | 0 | C | A | 39.4% | 172.6 / 49.8 | 104 | intergenic (+337/‑76) | BW25113_RS01680/BW25113_RS01685 | protein YahL/protein YahM |
| * | NZ_CP009273 | 3,344,212 | 0 | A | C | 39.2% | 140.4 / 13.4 | 74 | S725A (TCA→GCA) | arcB | aerobic respiration two‑component sensor histidine kinase ArcB |
| * | NZ_CP009273 | 2,897,051 | 0 | C | A | 39.1% | 165.8 / 61.9 | 87 | intergenic (+318/+1055) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 3,199,794 | 0 | C | T | 39.0% | 114.1 / 68.9 | 100 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 1,155,293 | 0 | A | G | 38.8% | 82.4 / 16.8 | 49 | I572T (ATC→ACC) | fhuE | ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE |
| * | NZ_CP009273 | 1,218,052 | 0 | G | A | 38.5% | 61.8 / 31.9 | 53 | F15F (TTC→TTT) | ymgD | YmgD family protein |
| * | NZ_CP009273 | 3,941,210 | 0 | C | T | 38.2% | 125.5 / 34.3 | 76 | E40K (GAA→AAA) | hdfR | HTH‑type transcriptional regulator HdfR |
| 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 | = 3416707 | 63 (0.650) | 8 (0.370) +191 bp |
6/112 | 3.1 | 35.2% | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 3416716 = | 69 (0.710) | intergenic (+163/+68) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 52 (0.530) | 45 (0.460) | 37/494 | 4.6 | 46.2% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 53 (0.540) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 360104 = | 56 (0.570) | 37 (0.390) +AATTCC |
29/482 | 6.2 | 35.6% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 81 (0.830) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 692197 | 64 (0.660) | 5 (0.080) | 4/338 | 13.3 | 8.2% | intergenic (‑1/+15) | BW25113_RS03450/BW25113_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NZ_CP009273 | 692591 = | 68 (1.020) | intergenic (‑2/+378) | BW25113_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP009273 | = 360286 | 56 (0.570) | 9 (0.090) +AATTC |
9/484 | 13.8 | 13.6% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 61 (0.630) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 115 (1.180) | 6 (0.060) | 6/476 | 15.6 | 5.2% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 108 (1.150) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 61 (0.630) | 4 (0.040) +GAATTAATTCC |
4/472 | 17.0 | 5.6% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 4161677 = | 81 (0.830) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 4532499 = | 120 (1.230) | 4 (0.040) | 4/476 | 17.1 | 3.4% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 109 (1.160) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 360104 = | 56 (0.570) | 4 (0.040) +AATTCC |
4/482 | 17.3 | 5.8% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 76 (0.780) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||