mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 53 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,815,801 | 0 | A | . | 50.0% | 307.1 / inf | 148 | intergenic (‑33/+62) | pyrE/rph | orotate phosphoribosyltransferase/truncated RNase PH |
| * | NC_000913 | 2,405,556 | 0 | T | C | 42.4% | 103.4 / 241.5 | 172 | intergenic (‑484/+147) | nuoA/lrhA | NADH:quinone oxidoreductase subunit A/DNA‑binding transcriptional dual regulator LrhA |
| * | NC_000913 | 195,495 | 0 | A | G | 41.9% | 83.9 / 163.0 | 128 | E198G (GAG→GGG) | ispU | undecaprenyl diphosphate synthase |
| * | NC_000913 | 1,560,033 | 0 | C | T | 40.6% | 84.1 / 163.1 | 123 | A299A (GCG→GCA) | ddpB | putative D,D‑dipeptide ABC transporter membrane subunit DdpB |
| * | NC_000913 | 2,898,938 | 0 | T | C | 38.3% | 94.0 / 133.9 | 107 | I161V (ATC→GTC) | ygcU | putative FAD‑containing dehydrogenase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.9% | 592.7 / inf | 439 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,349,145 | 0 | A | C | 32.1% | 190.8 / 30.2 | 106 | F110V (TTC→GTC) | inaA | putative lipopolysaccharide kinase InaA |
| * | NC_000913 | 1,618,074 | 0 | T | G | 31.2% | 159.9 / 11.2 | 96 | G349G (GGT→GGG) | ydeA | L‑arabinose exporter |
| * | NC_000913 | 987,494 | 0 | T | G | 30.5% | 216.5 / 17.0 | 97 | intergenic (‑512/+91) | ompF/asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| * | NC_000913 | 4,622,250 | 0 | A | G | 30.3% | 177.0 / 24.7 | 89 | E161G (GAG→GGG) | yjjJ | toxin YjjJ |
| * | NC_000913 | 1,701,310 | 0 | A | C | 30.2% | 210.1 / 11.5 | 97 | T118T (ACA→ACC) | malY | negative regulator of MalT activity/cystathionine beta‑lyase |
| * | NC_000913 | 3,873,886 | 0 | T | G | 30.2% | 266.9 / 19.6 | 130 | T197P (ACG→CCG) | dgoK | 2‑dehydro‑3‑deoxygalactonokinase |
| * | NC_000913 | 4,331,790 | 0 | T | G | 29.8% | 165.5 / 18.9 | 84 | V430G (GTT→GGT) | proP | osmolyte:H(+) symporter ProP |
| * | NC_000913 | 3,720 | 0 | T | G | 29.7% | 262.8 / 20.0 | 129 | V307G (GTA→GGA) | thrB | homoserine kinase |
| * | NC_000913 | 3,423,287 | 0 | G | C | 28.9% | 81.8 / 15.4 | 45 | intergenic (+93/+136) | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA |
| * | NC_000913 | 3,350,853 | 0 | A | C | 28.7% | 280.4 / 28.4 | 144 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| * | NC_000913 | 3,585,086 | 0 | A | C | 28.6% | 192.5 / 12.3 | 84 | Y580D (TAC→GAC) | ggt | glutathione hydrolase proenzyme |
| * | NC_000913 | 4,070,462 | 0 | T | C | 28.3% | 178.0 / 95.1 | 113 | intergenic (‑61/+53) | yihR/yihS | putative aldose 1‑epimerase YihR/sulfoquinovose isomerase |
| * | NC_000913 | 4,070,483 | 0 | A | G | 28.1% | 115.0 / 23.4 | 57 | intergenic (‑82/+32) | yihR/yihS | putative aldose 1‑epimerase YihR/sulfoquinovose isomerase |
| * | NC_000913 | 705,540 | 0 | C | A | 26.4% | 259.9 / 25.5 | 106 | P533T (CCG→ACG) | nagE | N‑acetylglucosamine specific PTS enzyme IIABC component |
| Marginal new junction evidence (lowest skew 10 of 40 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4422218 | 171 (1.130) | 14 (0.120) | 14/78 | 2.5 | 11.0% | coding (33/651 nt) | ulaD | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD |
| ? | NC_000913 | 4422486 = | 92 (0.770) | coding (301/651 nt) | ulaD | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD | |||||
| * | ? | NC_000913 | = 4400288 | 176 (1.160) | 14 (0.100) | 13/94 | 3.3 | 7.8% | coding (1/309 nt) | hfq | RNA‑binding protein Hfq |
| ? | NC_000913 | 4400296 = | 162 (1.110) | coding (9/309 nt) | hfq | RNA‑binding protein Hfq | |||||
| * | ? | NC_000913 | = 3618950 | 65 (0.430) | 12 (0.100) | 10/78 | 3.4 | 17.8% | coding (363/402 nt) | nikR | DNA‑binding transcriptional repressor NikR |
| ? | NC_000913 | 3625890 = | 59 (0.490) | coding (914/1125 nt) | yhhJ | ABC transporter family protein YhhJ | |||||
| * | ? | NC_000913 | = 3337461 | 156 (1.030) | 9 (0.070) | 9/78 | 3.6 | 7.2% | coding (431/636 nt) | mlaC | intermembrane phospholipid transport system ‑ periplasmic binding protein |
| ? | NC_000913 | 3337677 = | 107 (0.890) | coding (215/636 nt) | mlaC | intermembrane phospholipid transport system ‑ periplasmic binding protein | |||||
| * | ? | NC_000913 | = 3256322 | 85 (0.560) | 9 (0.080) | 7/76 | 4.1 | 14.0% | coding (330/1311 nt) | cyuA | putative L‑cysteine desulfidase CyuA |
| ? | NC_000913 | 3256551 = | 45 (0.380) | coding (101/1311 nt) | cyuA | putative L‑cysteine desulfidase CyuA | |||||
| * | ? | NC_000913 | = 2818077 | 90 (0.590) | 6 (0.070) | 4/58 | 4.3 | 7.1% | noncoding (59/77 nt) | argZ | tRNA‑Arg |
| ? | NC_000913 | 2818358 = | 105 (1.190) | intergenic (‑84/+115) | argY/argV | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | 2817923 = | 191 (1.260) | 7 (0.080) | 4/58 | 4.3 | 6.5% | intergenic (‑63/+136) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | = 2818057 | 90 (1.020) | intergenic (‑197/+2) | argQ/argZ | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | = 631287 | 36 (0.240) | 6 (0.050) | 6/72 | 4.3 | 14.1% | coding (1394/2106 nt) | cstA | carbon starvation protein A |
| ? | NC_000913 | 631525 = | 47 (0.430) | coding (1632/2106 nt) | cstA | carbon starvation protein A | |||||
| * | ? | NC_000913 | = 69441 | 72 (0.470) | 6 (0.050) | 6/78 | 4.5 | 8.7% | coding (608/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 69641 = | 69 (0.570) | coding (408/1701 nt) | araB | ribulokinase | |||||
| * | ? | NC_000913 | = 3613076 | 110 (0.730) | 5 (0.040) | 5/74 | 4.7 | 6.3% | coding (108/588 nt) | acpT | holo‑[acyl carrier protein] synthase 2 |
| ? | NC_000913 | 3613284 = | 67 (0.590) | coding (316/588 nt) | acpT | holo‑[acyl carrier protein] synthase 2 | |||||