mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 120 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 390,138 | 0 | A | C | 74.8% | 218.7 / 115.4 | 127 | intergenic (‑411/‑113) | hemB/yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| * | NC_000913 | 1,731,980 | 0 | A | C | 73.9% | 115.2 / 48.3 | 65 | E965A (GAA→GCA) | lhr | putative ATP‑dependent helicase |
| * | NC_000913 | 1,878,331 | 0 | T | G | 73.7% | 56.3 / 20.8 | 39 | I206R (ATA→AGA) | yeaP | diguanylate cyclase |
| * | NC_000913 | 3,720,069 | 0 | T | G | 73.5% | 284.1 / 152.4 | 170 | G7G (GGT→GGG) | cspA | RNA chaperone and antiterminator, cold‑inducible |
| * | NC_000913 | 3,517,396 | 0 | T | G | 73.3% | 209.2 / 124.9 | 131 | intergenic (‑90/+2) | damX/aroB | cell division protein that binds to the septal ring/3‑dehydroquinate synthase |
| * | NC_000913 | 145,789 | 0 | A | C | 72.0% | 159.9 / 99.8 | 107 | T237P (ACC→CCC) | yadE | putative polysaccharide deacetylase lipoprotein |
| * | NC_000913 | 394,101 | 0 | A | C | 71.5% | 162.8 / 113.4 | 116 | pseudogene (1132/1449 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| * | NC_000913 | 585,925 | 0 | A | C | 71.3% | 162.2 / 111.4 | 108 | intergenic (‑292/‑132) | ompT/pauD | DLP12 prophage; outer membrane protease VII; outer membrane protein 3b/tRNA‑OTHER |
| * | NC_000913 | 4,359,411 | 0 | A | C | 70.5% | 172.6 / 139.4 | 129 | A207A (GCT→GCG) | cadB | putative lysine/cadaverine transporter |
| * | NC_000913 | 193,432 | 0 | T | G | 70.2% | 108.2 / 87.9 | 84 | intergenic (+3/‑89) | frr/dxr | ribosome recycling factor/1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| * | NC_000913 | 3,655,257 | 0 | A | C | 69.3% | 103.4 / 108.4 | 101 | *216E (TAA→GAA) | yhiD | putative Mg(2+) transport ATPase, inner membrane protein |
| * | NC_000913 | 4,571,836 | 0 | T | G | 68.9% | 125.1 / 112.2 | 104 | M29R (ATG→AGG) | yjiS | DUF1127 family protein |
| * | NC_000913 | 1,355,049 | 0 | A | C | 68.8% | 77.8 / 79.0 | 77 | L141W (TTG→TGG) | sapB | antimicrobial peptide transport ABC transporter permease |
| * | NC_000913 | 3,318,766 | 0 | A | C | 67.9% | 110.3 / 127.9 | 109 | N44H (AAC→CAC) | argG | argininosuccinate synthetase |
| * | NC_000913 | 3,780,956 | 0 | A | C | 67.3% | 49.3 / 49.9 | 52 | Q377P (CAG→CCG) | lldD | L‑lactate dehydrogenase, FMN‑linked |
| * | NC_000913 | 3,860,764 | 0 | T | G | 67.3% | 109.9 / 129.5 | 107 | F161C (TTT→TGT) | yidL | AraC family putative transcriptional regulator |
| * | NC_000913 | 4,172,437 | 0 | A | C | 67.3% | 110.0 / 132.6 | 113 | V127V (GTA→GTC) | murB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| * | NC_000913 | 2,060,593 | 0 | A | C | 67.0% | 102.4 / 107.1 | 94 | L108V (TTG→GTG) | cbl | ssuEADCB/tauABCD operon transcriptional activator |
| * | NC_000913 | 1,155,360 | 0 | T | G | 67.0% | 99.5 / 114.9 | 103 | V79V (GTT→GTG) | tmk | thymidylate kinase |
| * | NC_000913 | 4,501,428 | 0 | A | C | 66.3% | 99.0 / 95.1 | 89 | T57P (ACT→CCT) | yjgZ | uncharacterized protein |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 857644 | 89 (0.990) | 8 (0.090) | 5/346 | 5.4 | 8.6% | noncoding (29/98 nt) | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 857679 | NA (NA) | noncoding (64/98 nt) | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP79 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 3089881 | 93 (1.030) | 4 (0.050) | 4/342 | 5.7 | 4.9% | coding (127/498 nt) | yggI | Zn‑dependent metalloprotease‑related protein |
| ? | NC_000913 | = 3090071 | 67 (0.780) | coding (317/498 nt) | yggI | Zn‑dependent metalloprotease‑related protein | |||||
| * | ? | NC_000913 | 2077808 = | 118 (1.310) | 4 (0.050) | 4/336 | 5.7 | 3.3% | coding (240/375 nt) | cbtA | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 126 (1.500) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 780619 = | 124 (1.380) | 5 (0.060) | 4/346 | 5.8 | 4.5% | noncoding (66/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 781584 = | 95 (1.100) | noncoding (8/76 nt) | lysQ | tRNA‑Lys | |||||
| * | ? | NC_000913 | = 4498394 | 2 (0.020) | 5 (0.060) | 3/338 | 6.2 | 72.7% | noncoding (214/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4498760 | NA (NA) | noncoding (580/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 3186309 | 5 (0.060) | 5 (0.060) | 3/338 | 6.2 | 51.6% | noncoding (214/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3186675 | NA (NA) | noncoding (580/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 2997112 = | NA (NA) | 5 (0.060) | 3/338 | 6.2 | 100% | noncoding (580/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2997478 = | 0 (0.000) | noncoding (214/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2331858 | 74 (0.820) | 4 (0.050) | 3/344 | 6.2 | 5.3% | pseudogene (2545/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| ? | NC_000913 | = 2331859 | 73 (0.850) | pseudogene (2544/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein | |||||
| * | ? | NC_000913 | 2069692 = | NA (NA) | 5 (0.060) | 3/338 | 6.2 | 72.7% | noncoding (580/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2070058 = | 2 (0.020) | noncoding (214/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1697979 | 65 (0.720) | 4 (0.050) | 3/346 | 6.2 | 6.1% | coding (62/768 nt) | hdhA | 7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent |
| ? | NC_000913 | = 1698127 | 60 (0.690) | intergenic (‑87/+25) | hdhA/malI | 7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent/transcriptional repressor of Mal regulon | |||||