mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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_012971 | 846,248 | 0 | G | T | 42.9% | 48.9 / 12.1 | 56 | S93Y (TCC→TAC) | ybiW | glycyl radical protein |
| * | NC_012971 | 62,261 | 0 | C | A | 38.0% | 135.5 / 30.9 | 108 | P234P (CCC→CCA) | djlA | co‑chaperone DjlA |
| * | NC_012971 | 1,337,830 | 0 | C | A | 37.5% | 114.1 / 19.8 | 88 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein |
| * | NC_012971 | 1,581,200 | 0 | G | T | 32.6% | 143.0 / 12.5 | 95 | pseudogene (383/1284 nt) | ydfJ | MHS family MFS transporter YdfJ |
| * | NC_012971 | 244,640 | 0 | C | A | 32.1% | 179.1 / 10.6 | 106 | E42* (GAG→TAG) | yafV | 2‑oxoglutaramate amidase |
| * | NC_012971 | 2,727,510 | 0 | G | T | 32.0% | 141.9 / 12.3 | 75 | P144Q (CCG→CAG) | ygcQ | electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_012971 | 2,589,438 | 0 | G | T | 30.8% | 210.9 / 16.1 | 117 | E38* (GAG→TAG) | pssA | CDP‑diacylglycerol‑‑serine O‑phosphatidyltransferase |
| * | NC_012971 | 2,016,684 | 0 | G | T | 30.6% | 111.7 / 16.2 | 72 | L251L (CTC→CTA) | wcaK | colanic acid biosynthesis pyruvyl transferase WcaK |
| * | NC_012971 | 1,006,183 | 0 | G | T | 29.5% | 155.4 / 13.7 | 95 | E627* (GAG→TAG) | elfC | fimbrial biogenesis usher protein |
| * | NC_012971 | 403,189 | 0 | G | T | 28.9% | 173.4 / 10.9 | 90 | L116L (CTC→CTA) | yajO | 1‑deoxyxylulose‑5‑phosphate synthase YajO |
| * | NC_012971 | 2,134,898 | 0 | G | T | 28.8% | 266.2 / 18.0 | 125 | pseudogene (350/994 nt) | mglB | galactose/glucose ABC transporter substrate‑binding protein MglB |
| * | NC_012971 | 1,456,833 | 0 | T | C | 28.7% | 148.1 / 26.6 | 87 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing protein |
| * | NC_012971 | 4,268,051 | 0 | C | A | 28.6% | 332.7 / 17.9 | 161 | E324* (GAG→TAG) | cadC | lysine decarboxylation/transport transcriptional activator CadC |
| * | NC_012971 | 3,561,696 | 0 | A | G | 28.2% | 118.3 / 36.9 | 71 | G21G (GGT→GGC) | ECD_RS25800 | type I toxin‑antitoxin system toxin Ldr family protein |
| * | NC_012971 | 3,800,334 | 0 | C | A | 28.0% | 314.5 / 12.4 | 168 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter substrate‑binding protein PstS/glutamine‑‑fructose‑6‑phosphate transaminase (isomerizing) |
| * | NC_012971 | 4,283,488 | 0 | C | A | 27.9% | 195.3 / 14.4 | 129 | L32L (CTC→CTA) | ecnA | lipoprotein antitoxin entericidin A |
| * | NC_012971 | 2,217,074 | 0 | C | A | 27.6% | 153.3 / 10.2 | 87 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_012971 | 2,314,969 | 0 | C | A | 27.5% | 166.9 / 11.6 | 91 | E26* (GAG→TAG) | argT | lysine/arginine/ornithine ABC transporter substrate‑binding protein ArgT |
| * | NC_012971 | 3,706,612 | 0 | G | T | 27.0% | 251.3 / 13.5 | 148 | E309* (GAG→TAG) | ECD_RS18380 | tetratricopeptide repeat protein |
| * | NC_012971 | 622,651 | 0 | C | A | 26.3% | 248.8 / 10.7 | 118 | intergenic (‑11/+90) | lipB/ybeD | lipoyl(octanoyl) transferase LipB/DUF493 family protein YbeD |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_012971 | = 739579 | 56 (0.580) | 21 (0.290) | 14/438 | 3.4 | 28.9% | noncoding (76/76 nt) | ECD_RS03630 | tRNA‑Lys |
| ? | NC_012971 | 740008 = | 62 (0.870) | intergenic (+1/‑132) | ECD_RS03645/ECD_RS03650 | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_012971 | = 2519344 | 107 (1.110) | 20 (0.230) | 17/540 | 3.7 | 16.1% | intergenic (+84/‑582) | ECD_RS25300/timP | IS3‑like element ISEcB1 family transposase/small toxic inner membrane protein TimP |
| ? | NC_012971 | 2519671 = | 110 (1.250) | intergenic (+411/‑255) | ECD_RS25300/timP | IS3‑like element ISEcB1 family transposase/small toxic inner membrane protein TimP | |||||
| * | ? | NC_012971 | = 739785 | 65 (0.680) | 13 (0.180) | 13/438 | 3.7 | 19.1% | noncoding (76/76 nt) | ECD_RS03640 | tRNA‑Lys |
| ? | NC_012971 | 740008 = | 62 (0.870) | intergenic (+1/‑132) | ECD_RS03645/ECD_RS03650 | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_012971 | = 1275121 | 54 (0.560) | 12 (0.180) | 11/416 | 4.0 | 25.5% | intergenic (‑1/+34) | ECD_RS06435/ECD_RS22720 | tRNA‑Tyr/RtT sRNA |
| ? | NC_012971 | 1275416 = | 32 (0.470) | intergenic (‑2/+158) | ECD_RS06440/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_012971 | = 740009 | 95 (0.990) | 12 (0.170) | 10/434 | 4.5 | 14.3% | intergenic (+2/‑131) | ECD_RS03645/ECD_RS03650 | tRNA‑Lys/tRNA‑Lys |
| ? | NC_012971 | 740218 = | 74 (1.050) | intergenic (+3/‑275) | ECD_RS03650/nadA | tRNA‑Lys/quinolinate synthase NadA | |||||
| * | ? | NC_012971 | = 739290 | 88 (0.920) | 12 (0.170) | 9/438 | 4.9 | 18.4% | noncoding (76/76 nt) | ECD_RS03620 | tRNA‑Lys |
| ? | NC_012971 | 739580 = | 41 (0.580) | intergenic (+1/‑51) | ECD_RS03630/ECD_RS03635 | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_012971 | = 4524541 | 88 (0.920) | 8 (0.120) | 7/412 | 5.3 | 12.1% | intergenic (‑1/+34) | ECD_RS22405/ECD_RS22410 | tRNA‑Leu/tRNA‑Leu |
| ? | NC_012971 | 4524778 = | 55 (0.820) | intergenic (‑2/+266) | ECD_RS22415/rsmC | tRNA‑Leu/16S rRNA (guanine(1207)‑N(2))‑methyltransferase RsmC | |||||
| * | ? | NC_012971 | = 2658241 | 43 (0.450) | 7 (0.100) | 7/432 | 5.5 | 14.4% | intergenic (‑1/+198) | ECD_RS13275/ECD_RS13280 | tRNA‑Arg/tRNA‑Arg |
| ? | NC_012971 | 2658517 = | 52 (0.740) | intergenic (‑2/+2) | ECD_RS13280/ECD_RS13285 | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NC_012971 | 1099967 = | 48 (0.500) | 8 (0.080) | 8/588 | 6.8 | 7.7% | intergenic (‑247/+164) | ECD_RS05470/ECD_RS05485 | IS3‑like element IS3 family transposase/tRNA‑Ser |
| ? | NC_012971 | 2827816 = | 144 (1.500) | coding (552/570 nt) | ECD_RS14080 | hypothetical protein | |||||
| * | ? | NC_012971 | 1099967 = | 48 (0.500) | 8 (0.080) | 8/590 | 6.8 | 14.3% | intergenic (‑247/+164) | ECD_RS05470/ECD_RS05485 | IS3‑like element IS3 family transposase/tRNA‑Ser |
| ? | NC_012971 | 1426589 = | NA (NA) | pseudogene (12/1965 nt) | tynA | primary‑amine oxidase | |||||