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 41 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,750,217 | 0 | G | A | 76.7% | 181.9 / 54.8 | 86 | D164D (GAC→GAT) | grpE | nucleotide exchange factor GrpE |
| * | NC_000913 | 186,117 | 0 | G | A | 70.0% | 195.9 / 94.7 | 111 | A845V (GCC→GTC) | glnD | protein‑PII uridylyltransferase/uridylyl‑removing enzyme |
| * | NC_000913 | 1,097,158 | 0 | C | T | 43.3% | 20.6 / 31.7 | 30 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,767,445 | 0 | C | A | 33.6% | 202.9 / 14.9 | 110 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 4,296,191 | 0 | A | C | 33.3% | 20.4 / 12.2 | 24 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,767,444 | 0 | C | A | 31.8% | 213.4 / 11.4 | 110 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,073,613 | 0 | G | T | 31.5% | 161.9 / 14.4 | 89 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 2,477,265 | 0 | A | C | 31.2% | 210.3 / 41.2 | 109 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,970,253 | 0 | G | T | 31.1% | 187.4 / 17.2 | 107 | E41* (GAG→TAG) | wecB | UDP‑N‑acetylglucosamine 2‑epimerase |
| * | NC_000913 | 3,054,886 | 0 | G | T | 30.5% | 193.0 / 26.1 | 105 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,669,715 | 0 | G | T | 29.7% | 188.8 / 17.7 | 118 | E42* (GAG→TAG) | treF | cytoplasmic trehalase |
| * | NC_000913 | 1,097,118 | 0 | C | A | 29.6% | 43.4 / 11.1 | 27 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,054,894 | 0 | G | T | 29.5% | 177.9 / 27.3 | 107 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 430,299 | 0 | C | A | 29.2% | 193.2 / 11.3 | 97 | F265L (TTC→TTA) | secF | Sec translocon accessory complex subunit SecF |
| * | NC_000913 | 12,152 | 0 | G | T | 29.0% | 233.5 / 16.6 | 131 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 2,465,016 | 0 | C | A | 28.9% | 217.2 / 14.4 | 114 | intergenic (‑9/‑285) | mlaA/yfdC | intermembrane phospholipid transport system ‑ outer membrane lipoprotein MlaA/inner membrane protein YfdC |
| * | NC_000913 | 2,159,415 | 0 | C | G | 28.8% | 133.4 / 17.8 | 58 | L344V (CTG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 3,032,307 | 0 | C | T | 28.8% | 174.6 / 44.0 | 111 | T314M (ACG→ATG) | uacT | urate:H(+) symporter |
| * | NC_000913 | 186,408 | 0 | G | T | 28.6% | 136.4 / 68.5 | 84 | A748E (GCG→GAG) | glnD | protein‑PII uridylyltransferase/uridylyl‑removing enzyme |
| * | NC_000913 | 2,990,480 | 0 | C | A | 28.6% | 356.3 / 18.0 | 182 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1411899 = | 129 (1.210) | 16 (0.160) | 15/546 | 5.0 | 11.8% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 122 (1.250) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | = 2653419 | 94 (0.880) | 12 (0.120) | 12/548 | 5.9 | 11.4% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 100 (1.020) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | 4542682 = | 166 (1.550) | 16 (0.150) | 11/580 | 6.6 | 9.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 153 (1.470) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 177 (1.650) | 10 (0.100) | 10/580 | 6.9 | 5.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 153 (1.470) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 696741 | 89 (0.830) | 8 (0.100) | 6/442 | 7.0 | 11.5% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 57 (0.720) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 781222 | 67 (0.630) | 6 (0.080) | 6/446 | 7.1 | 10.3% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 54 (0.680) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 3648146 | 122 (1.140) | 4 (0.050) | 4/482 | 8.6 | 3.9% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 99 (1.150) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2521006 | 88 (0.820) | 3 (0.040) | 3/446 | 8.8 | 4.5% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521127 = | 61 (0.760) | intergenic (+1/‑46) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1287084 | 64 (0.600) | 5 (0.050) | 5/558 | 8.9 | 7.8% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 59 (0.590) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 3469049 | 89 (0.830) | 4 (0.040) | 4/582 | 9.7 | 3.9% | coding (805/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469353 = | 110 (1.060) | coding (501/2694 nt) | chiA | endochitinase | |||||