mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 4,410,044 | 1 | .→T | 18.5% | 18.8 0.0 ‑0.0 | 27 | intergenic (+38/‑89) | rlmB/yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| * | NC_000913 | 3,508,894 | 0 | G→A | 10.5% | 11.6 ‑4.9 0.0 | 96 | A307V (GCA→GTA) | yhfW | phosphopentomutase‑related metalloenzyme superfamily protein |
| * | NC_000913 | 3,799,290 | 0 | T→C | 100.0% | 3.7 | 3 | K8R (AAA→AGA) | waaU | lipopolysaccharide core biosynthesis |
| * | NC_000913 | 3,621,045 | 0 | T→G | 100.0% | 1.3 | 1 | D618E (GAT→GAG) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,622,197 | 0 | A→. | 100.0% | 1.3 | 1 | coding (3006/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,942,228 | 0 | T→A | 100.0% | 1.2 | 1 | noncoding (421/1542 nt) | rrsC | 16S ribosomal RNA of rrnC operon |
| * | NC_000913 | 2,729,757 | 0 | C→A | 100.0% | 1.1 | 1 | noncoding (1401/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| * | NC_000913 | 1,432,431 | 0 | A→C | 100.0% | 0.8 | 1 | E7D (GAA→GAC) | tfaR | Rac prophage; putative tail fiber assembly protein |
| * | NC_000913 | 2,101,925 | 0 | T→A | 100.0% | 0.7 | 1 | Q329H (CAA→CAT) | insH1 | IS5 transposase and trans‑activator |
| * | NC_000913 | 3,621,054 | 0 | A→G | 100.0% | 0.4 | 1 | G621G (GGA→GGG) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 3,622,180 | 0 | C→G | 100.0% | 0.3 | 1 | L997V (CTG→GTG) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 1,634,461 | 0 | T→A | 100.0% | ‑0.5 | 1 | E142V (GAG→GTG) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,462 | 0 | C→A | 100.0% | ‑0.5 | 1 | E142* (GAG→TAG) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,464 | 0 | C→A | 100.0% | ‑0.5 | 1 | S141I (AGT→ATT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,465 | 0 | T→A | 100.0% | ‑0.5 | 1 | S141C (AGT→TGT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,466 | 0 | G→A | 100.0% | ‑0.5 | 1 | A140A (GCC→GCT) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| * | NC_000913 | 1,634,467 | 0 | G→A | 100.0% | ‑0.5 | 1 | A140V (GCC→GTC) | tfaQ | Qin prophage; putative tail fibre assembly protein |
| Marginal mixed read alignment evidence... | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | change | freq | score | reads | annotation | genes | product | ||
| * | NC_000913 | 2,074,357 | 0 | C→. | 10.4% | 18.1 ‑0.4 ‑0.0 | 67 | coding (2819/3120 nt) | flu | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| * | NC_000913 | 4,296,060 | 0 | C→T | 26.4% | 97.0 ‑0.2 ‑0.3 | 129 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3619878 = | NA (NA) | 10 (0.110) | 7/286 | 8.3 | 100% | coding (687/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3619892 = | 0 (0.000) | coding (701/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3327193 = | 77 (0.810) | 6 (0.070) | 6/286 | 8.8 | 7.8% | coding (472/630 nt) | rlmE | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent |
| ? | NC_000913 | 3327230 = | 70 (0.790) | coding (435/630 nt) | rlmE | 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 3858205 | 113 (1.190) | 5 (0.060) | 5/278 | 9.2 | 4.8% | coding (200/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | = 3858228 | 93 (1.070) | coding (177/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 5 (0.060) | 4/286 | 10.0 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1329792 | 85 (0.900) | 4 (0.040) | 4/292 | 10.2 | 4.9% | coding (461/1050 nt) | sohB | inner membrane protein, S49 peptidase family protein |
| ? | NC_000913 | = 1329859 | 73 (0.800) | coding (528/1050 nt) | sohB | inner membrane protein, S49 peptidase family protein | |||||
| * | ? | NC_000913 | 2729457 = | 66 (0.700) | 4 (0.040) | 4/288 | 10.1 | 5.8% | intergenic (‑13/+159) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2729476 = | 67 (0.750) | intergenic (‑32/+140) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 1987441 | 90 (0.950) | 4 (0.050) | 3/284 | 10.7 | 4.7% | intergenic (+13/+66) | ftnB/yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein |
| ? | NC_000913 | = 1987450 | 80 (0.900) | intergenic (+22/+57) | ftnB/yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein | |||||
| * | ? | NC_000913 | = 3355606 | 79 (0.830) | 4 (0.040) | 3/288 | 10.8 | 4.7% | coding (882/4461 nt) | gltB | glutamate synthase, large subunit |
| ? | NC_000913 | = 3355642 | 87 (0.970) | coding (918/4461 nt) | gltB | glutamate synthase, large subunit | |||||
| * | ? | NC_000913 | 225456 = | 18 (0.190) | 3 (0.030) | 3/286 | 10.7 | 13.7% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | 225477 = | 21 (0.240) | intergenic (+20/‑23) | ileV/alaV | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | NC_000913 | 225456 = | 18 (0.190) | 3 (0.040) | 3/260 | 10.1 | 5.9% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518117 | 94 (0.990) | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala | |||||
| * | ? | NC_000913 | 225456 = | 18 (0.190) | 3 (0.040) | 3/258 | 10.0 | 5.4% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518231 | 107 (1.130) | noncoding (1/76 nt) | alaW | tRNA‑Ala | |||||
| * | ? | NC_000913 | 225456 = | 18 (0.190) | 3 (0.030) | 3/286 | 10.7 | 15.0% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 3427056 | NA (NA) | intergenic (‑23/+20) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 225468 = | 21 (0.220) | 3 (0.030) | 3/286 | 10.7 | 13.2% | intergenic (+11/‑32) | ileV/alaV | tRNA‑Ile/tRNA‑Ala |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 3 (0.030) | 3/286 | 10.7 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1997022 = | 55 (0.580) | 3 (0.030) | 3/284 | 10.7 | 5.0% | intergenic (‑190/+40) | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase |
| ? | NC_000913 | 1997051 = | 63 (0.710) | intergenic (‑219/+11) | sdiA/yecC | quorum‑sensing transcriptional activator/putative ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 2091589 | 84 (0.890) | 3 (0.030) | 3/286 | 10.7 | 3.3% | coding (493/1305 nt) | hisD | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| ? | NC_000913 | = 2091646 | 98 (1.100) | coding (550/1305 nt) | hisD | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase | |||||
| * | ? | NC_000913 | = 2518117 | 94 (0.990) | 3 (0.040) | 3/260 | 10.1 | 3.6% | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | = 2518231 | 107 (1.130) | 3 (0.040) | 3/258 | 10.0 | 3.2% | noncoding (1/76 nt) | alaW | tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | 2729457 = | 66 (0.700) | 4 (0.040) | 3/288 | 10.8 | 5.4% | intergenic (‑13/+159) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 4168340 | 77 (0.860) | intergenic (+140/‑32) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 2729468 = | 69 (0.730) | 4 (0.040) | 3/288 | 10.8 | 5.4% | intergenic (‑24/+148) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 4168351 | 75 (0.840) | intergenic (+151/‑21) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | = 2730046 | NA (NA) | 3 (0.030) | 3/302 | 11.1 | NA | noncoding (1112/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2730050 = | NA (NA) | noncoding (1108/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | 3060398 = | 81 (0.860) | 3 (0.030) | 3/288 | 10.8 | 3.7% | coding (646/894 nt) | argP | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| ? | NC_000913 | 3060457 = | 79 (0.880) | coding (705/894 nt) | argP | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor | |||||
| * | ? | NC_000913 | = 3427065 | NA (NA) | 3 (0.030) | 3/286 | 10.7 | NA | intergenic (‑32/+11) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 4067707 = | 97 (1.020) | 3 (0.030) | 3/286 | 10.7 | 3.3% | coding (1570/2037 nt) | yihQ | putative sulpholipid alpha‑glucosidase; alpha‑glucosyl fluoride glucosidase |
| ? | NC_000913 | 4067734 = | 83 (0.930) | coding (1543/2037 nt) | yihQ | putative sulpholipid alpha‑glucosidase; alpha‑glucosyl fluoride glucosidase | |||||