mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 56 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,067,300 | 0 | C | T | 53.9% | 52.5 / inf | 217 | intergenic (‑15/‑1335) | insH6/yoeA | IS5 family transposase and trans‑activator/TonB‑dependent receptor plug domain‑containing protein YoeA |
| * | NC_000913 | 4,037,496 | 0 | A | T | 51.2% | 49.6 / inf | 202 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 2,477,265 | 0 | A | C | 40.6% | 191.6 / 49.6 | 128 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 38.1% | 109.5 / 38.8 | 97 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 58,065 | 0 | C | A | 37.7% | 144.2 / 28.1 | 106 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 2,767,445 | 0 | C | A | 37.5% | 186.2 / 25.7 | 113 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,054,886 | 0 | G | T | 37.5% | 128.3 / 39.1 | 96 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 449,461 | 0 | C | A | 37.2% | 46.1 / 24.3 | 43 | G394V (GGC→GTC) | cyoB | cytochrome bo3 subunit 1 |
| * | NC_000913 | 1,351,463 | 0 | C | A | 37.1% | 117.9 / 18.7 | 97 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 3,054,888 | 0 | A | C | 34.8% | 145.6 / 12.2 | 96 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 915,190 | 0 | C | T | 34.0% | 83.8 / 11.1 | 54 | intergenic (‑333/+162) | lysO/aqpZ | L‑lysine/thialysine exporter/water channel AqpZ |
| * | NC_000913 | 2,767,444 | 0 | C | A | 33.6% | 208.5 / 19.5 | 113 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,722,838 | 0 | G | T | 31.7% | 204.6 / 11.6 | 104 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 2,767,443 | 0 | C | A | 31.2% | 209.0 / 17.8 | 113 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,911,533 | 0 | C | A | 30.0% | 310.9 / 25.8 | 170 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,457,177 | 0 | T | G | 29.8% | 117.3 / 11.1 | 68 | G661G (GGA→GGC) | fadJ | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| * | NC_000913 | 939,398 | 0 | C | A | 29.7% | 200.6 / 16.0 | 101 | intergenic (+61/‑30) | rarA/serS | replication‑associated recombination protein A/serine‑‑tRNA ligase |
| * | NC_000913 | 225,579 | 0 | C | A | 28.1% | 175.8 / 16.0 | 121 | intergenic (+4/‑180) | alaV/rrlH | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 847,955 | 0 | G | A | 27.9% | 215.1 / 39.7 | 136 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,767,447 | 0 | C | A | 27.5% | 253.0 / 12.4 | 121 | intergenic (+92/‑263) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 689045 | NA (NA) | 31 (0.270) | 24/598 | 3.6 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 803442 | 0 (0.000) | intergenic (+122/‑61) | ybhI/ybhJ | putative tricarboxylate transporter/putative hydratase YbhJ | |||||
| * | ? | NC_000913 | = 568034 | NA (NA) | 21 (0.180) | 18/596 | 4.7 | 13.1% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 569137 = | 139 (1.220) | coding (236/1527 nt) | ybcK | putative recombinase YbcK | |||||
| * | ? | NC_000913 | = 4606166 | 153 (1.340) | 12 (0.150) | 10/420 | 5.0 | 10.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 91 (1.130) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 2470041 = | 139 (1.220) | 18 (0.160) | 16/598 | 5.2 | 11.5% | coding (911/1332 nt) | yfdI | serotype‑specific glucosyl transferase YfdI |
| ? | NC_000913 | = 3131340 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3361275 | 104 (0.910) | 19 (0.170) | 15/598 | 5.4 | 15.4% | coding (100/765 nt) | gltF | periplasmic protein GltF |
| ? | NC_000913 | 3365556 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 15 (0.130) | 14/598 | 5.7 | 7.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2774956 | 174 (1.520) | coding (1639/1704 nt) | yfjW | uncharacterized protein YfjW | |||||
| * | ? | NC_000913 | = 780918 | 54 (0.470) | 9 (0.110) | 9/446 | 5.7 | 19.1% | noncoding (76/76 nt) | lysW | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 36 (0.420) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 696469 | 87 (0.760) | 17 (0.150) +T |
14/596 | 5.7 | 16.0% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696583 = | 92 (0.810) | noncoding (34/75 nt) | glnV | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 15 (0.130) | 12/594 | 6.2 | 11.3% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2320016 = | 118 (1.040) | intergenic (‑140/‑27) | rcsC/atoS | histidine kinase RcsC/sensor histidine kinase AtoS | |||||
| * | ? | NC_000913 | 926551 = | 128 (1.130) | 13 (0.110) | 12/594 | 6.2 | 9.2% | intergenic (‑108/+177) | infA/aat | translation initiation factor IF‑1/leucyl/phenylalanyl‑tRNA‑‑protein transferase |
| ? | NC_000913 | = 1095502 | NA (NA) | noncoding (1/1258 nt) | IS3 | repeat region | |||||