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 64 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,166,873 | 0 | C | T | 71.0% | 21.9 / 23.6 | 38 | noncoding (215/1542 nt) | rrsB | 16S ribosomal RNA |
| * | NC_000913 | 2,690,005 | 0 | A | C | 48.3% | ‑5.5 / 184.4 | 116 | L365R (CTG→CGG) | glrK | histidine kinase GlrK |
| * | NC_000913 | 1,371,421 | 0 | C | T | 40.5% | 101.3 / 159.2 | 131 | C402C (TGC→TGT) | ycjM | glucosylglycerate phosphorylase |
| * | NC_000913 | 3,054,894 | 0 | G | T | 40.0% | 113.1 / 39.4 | 105 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 37.8% | 232.1 / 30.3 | 156 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,767,445 | 0 | C | A | 37.5% | 185.6 / 26.9 | 112 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 4,136,467 | 0 | A | C | 37.5% | 114.5 / 19.2 | 80 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 2,477,265 | 0 | A | C | 33.8% | 142.1 / 19.7 | 80 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,073,613 | 0 | G | T | 33.3% | 143.7 / 16.3 | 97 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 3,054,886 | 0 | G | T | 33.3% | 171.0 / 37.0 | 105 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,457,177 | 0 | T | G | 31.8% | 98.6 / 11.1 | 65 | G661G (GGA→GGC) | fadJ | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| * | NC_000913 | 1,922,815 | 0 | C | A | 31.0% | 157.6 / 15.0 | 100 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 834,674 | 0 | C | A | 30.8% | 280.2 / 19.0 | 133 | L535L (CTC→CTA) | dinG | ATP‑dependent DNA helicase DinG |
| * | NC_000913 | 1,334,966 | 0 | A | C | 30.7% | 262.7 / 31.7 | 163 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 4,296,191 | 0 | A | C | 30.6% | 46.7 / 33.5 | 49 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,001,094 | 0 | G | T | 30.5% | 285.5 / 14.8 | 164 | E627* (GAG→TAG) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 3,226,224 | 0 | G | T | 30.3% | 235.2 / 20.5 | 145 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| * | NC_000913 | 1,097,118 | 0 | C | A | 30.0% | 102.1 / 38.3 | 70 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,671,531 | 0 | G | T | 29.7% | 153.3 / 10.5 | 101 | E103* (GAG→TAG) | hcaB | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| * | NC_000913 | 4,213,310 | 0 | G | T | 29.6% | 329.3 / 16.6 | 169 | G26V (GGA→GTA) | yjaA | stress response protein |
| Marginal new junction evidence (lowest skew 10 of 81 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 63 (0.510) | 33 (0.280) | 27/566 | 3.4 | 30.5% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 91 (0.780) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 896272 | 119 (0.970) | 24 (0.200) | 23/598 | 4.4 | 19.7% | coding (139/954 nt) | potH | putrescine ABC transporter membrane subunit PotH |
| ? | NC_000913 | 907727 = | 77 (0.630) | coding (556/1431 nt) | ybjT | putative NAD(P)‑binding protein YbjT | |||||
| * | ? | NC_000913 | = 3064082 | 135 (1.100) | 24 (0.200) | 21/598 | 4.7 | 15.1% | coding (90/786 nt) | scpB | methylmalonyl‑CoA decarboxylase |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 317763 | 152 (1.250) | 23 (0.190) | 20/594 | 4.9 | 13.1% | coding (557/594 nt) | rclC | DUF417 domain‑containing inner membrane protein RclC |
| ? | NC_000913 | 1469296 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 3648146 | 154 (1.260) | 14 (0.140) | 14/482 | 5.2 | 10.7% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 109 (1.100) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 3064081 = | 134 (1.100) | 23 (0.190) | 18/596 | 5.4 | 14.6% | coding (89/786 nt) | scpB | methylmalonyl‑CoA decarboxylase |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 20 (0.160) | 18/598 | 5.4 | 14.9% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 2445295 = | 114 (0.930) | coding (266/810 nt) | yfcA | putative transporter YfcA | |||||
| * | ? | NC_000913 | 317762 = | 159 (1.300) | 22 (0.180) | 18/598 | 5.4 | 12.2% | coding (558/594 nt) | rclC | DUF417 domain‑containing inner membrane protein RclC |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1999730 | 98 (0.800) | 22 (0.180) | 17/594 | 5.6 | 18.6% | coding (656/801 nt) | tcyJ | cystine ABC transporter periplasmic binding protein |
| ? | NC_000913 | 2025435 = | 95 (0.780) | intergenic (‑122/‑76) | dsrA/yedP | small regulatory RNA DsrA/putative mannosyl‑3‑phosphoglycerate phosphatase | |||||
| * | ? | NC_000913 | = 656016 | 144 (1.170) | 14 (0.110) | 14/598 | 6.4 | 8.9% | intergenic (‑48/‑541) | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/Lipid A palmitoyltransferase |
| ? | NC_000913 | 687851 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||