mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 259 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 49.1% | 45.5 / 18.9 | 53 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 3,199,794 | 0 | C | T | 41.9% | 60.1 / 52.7 | 74 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 2,319,929 | 0 | T | G | 41.1% | 136.2 / 13.6 | 73 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NZ_CP009273 | 3,394,818 | 0 | T | C | 39.8% | 143.5 / 33.8 | 93 | D625G (GAT→GGT) | csrD | RNase E specificity factor CsrD |
| * | NZ_CP009273 | 107,682 | 0 | T | G | 38.2% | 131.8 / 10.8 | 76 | V51G (GTG→GGG) | mutT | 8‑oxo‑dGTP diphosphatase MutT |
| * | NZ_CP009273 | 3,806,632 | 0 | C | T | 38.0% | 44.8 / 23.4 | 50 | S181L (TCG→TTG) | coaBC | bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC |
| * | NZ_CP009273 | 3,837,579 | 0 | T | G | 37.8% | 170.2 / 19.4 | 94 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NZ_CP009273 | 1,240,690 | 0 | G | T | 37.6% | 160.4 / 32.1 | 85 | L25F (TTG→TTT) | BW25113_RS06225 | protein YcgY |
| * | NZ_CP009273 | 3,199,811 | 0 | C | A | 36.8% | 89.2 / 37.2 | 79 | intergenic (‑196/‑11) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 3,199,803 | 0 | T | A | 36.7% | 84.9 / 28.5 | 79 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 2,821,865 | 0 | T | G | 36.2% | 108.2 / 26.4 | 80 | V257G (GTG→GGG) | srlD | sorbitol‑6‑phosphate dehydrogenase |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 35.9% | 53.1 / 12.8 | 53 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 2,089,571 | 0 | A | G | 35.3% | 117.9 / 18.3 | 68 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase subunit HisF |
| * | NZ_CP009273 | 2,221,729 | 0 | A | T | 35.1% | 73.7 / 17.7 | 58 | pseudogene (509/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NZ_CP009273 | 4,245,989 | 0 | C | T | 35.1% | 83.5 / 16.3 | 58 | E136K (GAA→AAA) | plsB | glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 34.4% | 137.0 / 14.0 | 64 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 3,199,805 | 0 | C | A | 34.2% | 89.0 / 20.3 | 80 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 1,429,984 | 0 | G | A | 34.2% | 150.2 / 40.9 | 82 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NZ_CP009273 | 4,326,718 | 0 | T | A | 32.9% | 135.5 / 22.1 | 79 | Y44F (TAT→TTT) | adiC | arginine/agmatine antiporter |
| * | NZ_CP009273 | 2,845,013 | 0 | T | G | 32.9% | 152.8 / 17.4 | 73 | G218G (GGT→GGG) | hypB | hydrogenase nickel incorporation protein HypB |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | 45 (0.440) | 48 (0.470) | 42/496 | 4.1 | 45.7% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 69 (0.680) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 360104 = | 51 (0.500) | 41 (0.410) +AATTCC |
35/484 | 5.2 | 38.9% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 81 (0.800) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 1203246 = | 60 (0.590) | 21 (0.220) | 21/464 | 8.6 | 22.3% | coding (290/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | 1205075 = | 90 (0.950) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | 3416618 = | 73 (0.720) | 9 (0.140) +93 bp |
9/310 | 9.5 | 15.9% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416707 | 79 (0.780) | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 1203261 | 56 (0.550) | 18 (0.190) | 18/464 | 9.7 | 20.2% | coding (305/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | = 1205058 | 90 (0.950) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 360286 | 70 (0.690) | 14 (0.140) +AATTC |
14/486 | 12.0 | 16.7% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 73 (0.720) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 73 (0.720) | 9 (0.090) +GAATTAATTCC |
9/474 | 14.4 | 10.9% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 4161677 = | 81 (0.800) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 51 (0.500) | 5 (0.050) +AATTCC |
5/484 | 17.4 | 6.4% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 100 (0.990) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||