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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,842,434 | 0 | C | T | 72.2% | 159.9 / 77.5 | 109 | W787* (TGG→TAG) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 549,164 | 0 | C | T | 69.9% | 93.4 / 58.4 | 74 | L672F (CTC→TTC) | fusA | elongation factor G 1 |
| * | NC_002947_CJ‑RC | 3,466,843 | 0 | C | G | 53.8% | 1.6 / 10.8 | 15 | intergenic (‑18/+106) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 53.3% | ‑0.6 / 11.1 | 18 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.1% | 9.2 / 147.1 | 111 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 3,466,841 | 0 | T | G | 52.6% | 8.5 / 23.5 | 20 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.9% | ‑0.0 / 158.0 | 113 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 50.9% | 4.2 / 170.1 | 114 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 50.0% | 2.4 / 13.6 | 22 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 44.4% | 3.2 / 10.1 | 29 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 43.8% | 126.0 / 192.3 | 153 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 38.0% | 30.8 / 15.3 | 52 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 36.0% | 45.7 / 17.2 | 52 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 35.7% | 16.6 / 10.2 | 44 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 32.2% | 97.3 / 13.9 | 59 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 1,403,591 | 0 | T | C | 31.0% | 19.9 / 19.8 | 33 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 117,276 | 0 | C | G | 29.4% | 86.5 / 14.2 | 51 | intergenic (+56/+38) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 1,898,993 | 0 | T | G | 29.3% | 77.3 / 10.5 | 41 | intergenic (+63/‑457) | PP_t18/PP_1703 | tRNA‑Asp/assimilatory nitrate reductase/sulfite reductase |
| * | NC_002947_CJ‑RC | 4,044,569 | 0 | A | C | 28.8% | 95.5 / 11.1 | 52 | V380G (GTG→GGG) | PP_3566 | MFS transporter |
| * | NC_002947_CJ‑RC | 1,403,590 | 0 | G | A | 27.3% | 48.0 / 18.4 | 33 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 1844137 | 60 (0.770) | 24 (0.320) | 21/282 | 4.5 | 24.7% | coding (657/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947_CJ‑RC | 2177702 = | 88 (1.160) | intergenic (+103/‑63) | PP_5485/PP_1931 | GNAT family acetyltransferase/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 64 (0.820) | 21 (0.310) | 17/250 | 4.7 | 43.2% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | 1844134 = | 59 (0.760) | 19 (0.250) | 19/280 | 5.0 | 21.3% | coding (660/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947_CJ‑RC | = 2179376 | 83 (1.100) | intergenic (+175/+93) | PP_1931/PP_5486 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 10 (0.130) | 19 (0.320) | 12/220 | 5.5 | 55.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 23 (0.390) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 18 (0.250) | 14/266 | 6.1 | 49.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 34 (0.480) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.530) | 17 (0.230) | 14/280 | 6.5 | 31.0% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 36 (0.480) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 16 (0.210) +GCC |
14/284 | 6.6 | 89.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 13 (0.190) | 9/250 | 7.6 | 43.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 31 (0.460) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 10 (0.130) +CGGG |
9/282 | 8.5 | 91.1% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.010) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 33 (0.420) | 6 (0.080) | 6/272 | 9.8 | 11.8% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 59 (0.810) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||