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 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP006881 | 2,992,488 | 0 | A | C | 69.7% | 3.2 / 26.9 | 85 | noncoding (2286/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 2,992,522 | 0 | T | C | 44.2% | ‑5.6 / 37.5 | 105 | noncoding (2252/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 2,992,467 | 0 | T | C | 40.0% | ‑2.9 / 11.0 | 70 | noncoding (2307/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 2,992,473 | 0 | A | C | 39.7% | ‑4.2 / 22.4 | 75 | noncoding (2301/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 2,992,454 | 0 | A | C | 39.7% | ‑4.2 / 10.3 | 60 | noncoding (2320/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 1,309,742 | 0 | A | G | 35.4% | 393.0 / 80.6 | 284 | intergenic (+27/‑26) | U712_06660/U712_06665 | Phage‑like element PBSX protein xepA/Protein xhlA |
| * | CP006881 | 2,992,541 | 0 | G | C | 32.4% | 1.9 / 19.8 | 108 | noncoding (2233/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 3,554,122 | 0 | A | G | 32.2% | 280.9 / 42.3 | 181 | I274V (ATC→GTC) | U712_18220 | putative ATP‑dependent helicase ywqA |
| * | CP006881 | 100,392 | 0 | T | G | 31.9% | 88.4 / 36.0 | 74 | noncoding (2286/2928 nt) | U712_20965 | 23S ribosomal RNA |
| * | CP006881 | 3,406,275 | 0 | T | C | 28.7% | 537.3 / 68.5 | 311 | I314V (ATC→GTC) | U712_17490 | ATP phosphoribosyltransferase regulatory subunit |
| * | CP006881 | 3,581,989 | 0 | A | C | 28.4% | 214.1 / 26.9 | 196 | *258E (TAA→GAA) | U712_18400 | HTH‑type transcriptional activator mta |
| * | CP006881 | 2,992,535 | 0 | A | G | 27.9% | 5.8 / 11.5 | 112 | noncoding (2239/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 1,051,269 | 0 | C | G | 27.3% | 293.2 / 29.1 | 198 | G13G (GGC→GGG) | U712_05170 | Protoporphyrinogen oxidase |
| * | CP006881 | 1,127,082 | 0 | A | G | 26.8% | 665.9 / 77.0 | 330 | S301G (AGC→GGC) | U712_05545 | HTH‑type transcriptional regulator degA |
| * | CP006881 | 2,909,161 | 0 | A | G | 26.8% | 454.3 / 53.8 | 247 | S62P (TCC→CCC) | U712_14990 | Biotin synthase |
| * | CP006881 | 1,216,190 | 0 | T | G | 26.4% | 435.7 / 41.5 | 196 | G18G (GGT→GGG) | U712_06090 | UPF0752 sporulation protein yjcZ |
| * | CP006881 | 2,443,500 | 0 | A | C | 26.2% | 600.7 / 66.5 | 266 | G89G (GGT→GGG) | U712_12455 | Chaperone protein DnaJ |
| * | CP006881 | 1,127,044 | 0 | T | C | 26.0% | 586.6 / 59.1 | 320 | L288P (CTG→CCG) | U712_05545 | HTH‑type transcriptional regulator degA |
| * | CP006881 | 2,992,509 | 0 | A | C | 25.5% | 7.8 / 12.3 | 103 | noncoding (2265/2928 nt) | U712_21375 | 23S ribosomal RNA |
| * | CP006881 | 474,635 | 0 | T | G | 25.1% | 391.3 / 25.1 | 170 | intergenic (+418/‑88) | U712_02190/U712_02195 | General stress protein 26/Uncharacterized protein ydaH |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | pSIJ663_pHT315_araE_xy | = 5614 | 0 (0.000) | 30 (0.000) | 27/292 | 12.6 | 95.2% | intergenic (+883/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9532 = | 3 (0.000) | intergenic (+4801/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5330 | 14770 (1.570) | 17 (0.000) +42 bp |
16/214 | 13.1 | 0.16% | intergenic (+599/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9875 = | NA (NA) | intergenic (+5144/–) | ampR/– | –/– | |||||
| * | ? | CP006881 | 9457 = | 243 (0.900) | 3310 (12.810) | 15/286 | 16.0 | 93.5% | coding (2464/2466 nt) | U712_00040 | DNA gyrase subunit A |
| ? | CP006881 | 3301929 = | 225 (0.870) | coding (1392/1395 nt) | U712_16990 | Arabinose‑proton symporter | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5534 | 1104 (0.120) | 14 (0.000) +TCCTTTTGCTCA |
13/274 | 16.7 | 1.4% | intergenic (+803/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9884 = | NA (NA) | intergenic (+5153/–) | ampR/– | –/– | |||||
| * | ? | CP006881 | = 3884280 | 281 (1.040) | 4 (0.020) | 4/288 | 21.6 | 1.5% | coding (219/354 nt) | U712_20025 | Uncharacterized protein yxeD |
| ? | CP006881 | 3884427 = | 263 (1.010) | intergenic (+12/+32) | U712_20025/U712_20030 | Uncharacterized protein yxeD/Uncharacterized protein yxeC | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 2731 = | 7594 (0.810) | 5 (0.000) | 5/292 | 21.8 | 0.051% | intergenic (–/‑247) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | 2939 = | 12177 (1.320) | intergenic (–/‑39) | –/eryR | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 3328 | 13591 (1.440) | 4 (0.000) | 4/284 | 22.2 | 0.029% | coding (351/738 nt) | eryR | |
| ? | pSIJ663_pHT315_araE_xy | = 3458 | 14202 (1.580) | coding (481/738 nt) | eryR | ||||||
| * | ? | CP006881 | = 1012980 | 246 (0.910) | 3 (0.010) | 3/280 | 22.2 | 1.3% | intergenic (‑20/+85) | U712_04955/U712_04960 | Hypothetical Protein/Hypothetical Protein |
| ? | CP006881 | = 1013000 | 242 (0.960) | intergenic (‑40/+65) | U712_04955/U712_04960 | Hypothetical Protein/Hypothetical Protein | |||||
| * | ? | CP006881 | 3301923 = | 232 (0.860) | 3327 (0.700) | 3/292 | 22.5 | 96.7% | intergenic (‑295/+3) | U712_16985/U712_16990 | Central glycolytic genes regulator/Arabinose‑proton symporter |
| ? | pSIJ663_pHT315_araE_xy | = 5650 | 0 (0.000) | intergenic (+919/–) | ampR/– | –/– | |||||
| * | ? | CP006881 | = 2922385 | 267 (0.990) | 3 (0.010) | 3/296 | 22.6 | 1.1% | coding (514/2415 nt) | U712_15050 | Leucyl‑tRNA synthetase |
| ? | CP006881 | 3895758 = | 293 (1.100) | coding (253/1317 nt) | U712_20085 | Minor myo‑inositol transporter iolF | |||||