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 32 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,166,849 | 0 | G | A | 52.9% | 1.4 / 48.8 | 34 | noncoding (191/1542 nt) | rrsB | 16S ribosomal RNA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 44.1% | 165.0 / 29.5 | 136 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,296,190 | 0 | A | G | 36.0% | 11.7 / 22.0 | 25 | intergenic (+396/+246) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,097,118 | 0 | C | A | 35.7% | 6.6 / 23.5 | 28 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 58,065 | 0 | C | A | 35.2% | 125.9 / 24.1 | 91 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 847,955 | 0 | G | A | 33.9% | 151.7 / 53.3 | 115 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 12,152 | 0 | G | T | 33.7% | 123.7 / 18.9 | 95 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 1,466,438 | 0 | T | G | 33.3% | 75.3 / 37.4 | 51 | pseudogene (1047/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 4,296,191 | 0 | A | C | 32.0% | 10.3 / 21.1 | 25 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 228,689 | 0 | T | . | 32.0% | 181.6 / 133.8 | 98 | intergenic (+27/‑67) | rrlH/rrfH | 23S ribosomal RNA/5S ribosomal RNA |
| * | NC_000913 | 320,845 | 0 | C | A | 31.8% | 111.2 / 10.1 | 88 | R207R (CGG→AGG) | rclR | DNA‑binding transcriptional activator RclR |
| * | NC_000913 | 1,466,432 | 0 | A | G | 31.4% | 78.8 / 38.3 | 51 | pseudogene (1041/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,288,418 | 0 | G | T | 30.5% | 195.7 / 13.9 | 118 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 2,073,613 | 0 | G | T | 29.3% | 90.5 / 13.4 | 58 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 1,466,280 | 0 | A | C | 28.3% | 70.4 / 22.6 | 46 | pseudogene (889/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 3,593,181 | 0 | G | T | 28.1% | 172.9 / 11.0 | 89 | P86Q (CCG→CAG) | livF | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF |
| * | NC_000913 | 1,272,420 | 0 | C | A | 27.8% | 168.5 / 15.2 | 90 | intergenic (+71/‑87) | chaB/chaC | putative cation transport regulator ChaB/glutathione‑specific gamma‑glutamylcyclotransferase |
| * | NC_000913 | 2,815,937 | 0 | G | T | 26.7% | 215.0 / 12.8 | 116 | S168* (TCG→TAG) | gshA | glutamate‑‑cysteine ligase |
| * | NC_000913 | 1,502,772 | 0 | G | A | 26.5% | 98.4 / 14.0 | 68 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 1,502,770 | 0 | T | C | 26.1% | 107.9 / 13.7 | 69 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 55 (0.710) | 4 (0.070) | 4/412 | 5.6 | 8.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 45 (0.830) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781222 | 60 (0.770) | 9 (0.120) | 7/554 | 5.6 | 12.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 2521485 = | 70 (0.960) | intergenic (+157/+108) | lysV/xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR | |||||
| * | ? | NC_000913 | = 696466 | 80 (1.030) | 7 (0.090) | 7/570 | 5.7 | 9.1% | noncoding (39/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696902 = | 62 (0.820) | noncoding (38/75 nt) | glnU | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 2653419 | 75 (0.960) | 6 (0.080) | 6/540 | 5.9 | 7.0% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 90 (1.260) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 4079197 | 126 (1.620) | 5 (0.070) | 5/546 | 6.4 | 4.4% | intergenic (+759/‑94) | fabY/yiiE | putative fatty acid biosynthesis enzyme FabY/putative DNA‑binding transcriptional regulator YiiE |
| ? | NC_000913 | 4079636 = | 103 (1.430) | intergenic (+127/‑115) | yiiE/yiiF | putative DNA‑binding transcriptional regulator YiiE/protein YiiF | |||||
| * | ? | NC_000913 | = 2521359 | 69 (0.890) | 4 (0.060) | 4/492 | 6.4 | 6.2% | intergenic (+31/+234) | lysV/xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| ? | NC_000913 | 2521516 = | 64 (0.990) | intergenic (+188/+77) | lysV/xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR | |||||
| * | ? | NC_000913 | = 3469013 | 113 (1.450) | 5 (0.070) | 5/574 | 6.6 | 4.6% | coding (841/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469317 = | 98 (1.290) | coding (537/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 2877772 | 64 (0.820) | 3 (0.040) | 3/568 | 7.7 | 4.2% | intergenic (+154/+797) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| ? | NC_000913 | 2878263 = | 75 (1.000) | intergenic (+645/+306) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 | |||||
| * | ? | NC_000913 | = 2576868 | 76 (0.980) | 4 (0.050) | 3/568 | 7.7 | 5.1% | coding (1510/2280 nt) | maeB | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) |
| ? | NC_000913 | 2577226 = | 75 (1.000) | coding (1152/2280 nt) | maeB | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) | |||||
| * | ? | NC_000913 | = 1950744 | 93 (1.190) | 3 (0.040) | 3/566 | 7.7 | 3.4% | intergenic (‑222/‑88) | aspS/yecD | aspartate‑‑tRNA ligase/isochorismatase family protein YecD |
| ? | NC_000913 | 1951075 = | 81 (1.080) | coding (244/567 nt) | yecD | isochorismatase family protein YecD | |||||