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 116 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,633,993 | 0 | G | A | 63.2% | ‑5.7 / 13.4 | 19 | pseudogene (399/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,633,996 | 0 | G | A | 63.2% | ‑5.7 / 15.1 | 19 | pseudogene (396/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,633,998 | 0 | T | C | 63.2% | ‑5.7 / 17.5 | 19 | pseudogene (394/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,633,999 | 0 | C | T | 63.2% | ‑5.7 / 12.5 | 19 | pseudogene (393/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 580,498 | 0 | G | A | 61.4% | 67.8 / 197.3 | 158 | V148I (GTT→ATT) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,634,002 | 0 | G | A | 60.0% | ‑5.3 / 20.1 | 20 | pseudogene (390/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,634,005 | 0 | G | A | 60.0% | ‑5.4 / 18.9 | 20 | pseudogene (387/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,633,984 | 0 | C | A | 55.6% | ‑5.4 / 11.2 | 18 | pseudogene (408/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 580,509 | 0 | G | C | 54.4% | 226.3 / inf | 270 | L151L (CTG→CTC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,633,966 | 0 | T | C | 53.8% | ‑5.7 / 10.7 | 13 | pseudogene (426/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,633,972 | 0 | A | G | 52.9% | ‑5.0 / 20.4 | 17 | pseudogene (420/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,633,975 | 0 | A | G | 52.9% | ‑5.1 / 12.4 | 17 | pseudogene (417/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 580,512 | 0 | A | G | 52.9% | 232.7 / inf | 278 | K152K (AAA→AAG) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,518 | 0 | T | C | 49.6% | 383.1 / inf | 363 | D154D (GAT→GAC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,524 | 0 | C | T | 48.5% | 420.7 / inf | 375 | I156I (ATC→ATT) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,513 | 0 | C | A | 48.2% | 360.5 / inf | 305 | R153R (CGG→AGG) ‡ | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,356 | 0 | T | C | 48.2% | 93.7 / inf | 1086 | S167S (AGT→AGC) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,514 | 0 | G | A | 47.9% | 364.5 / inf | 309 | R153Q (CGG→CAG) ‡ | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,425 | 0 | T | A | 47.7% | 169.2 / 255.4 | 155 | G123G (GGT→GGA) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,359 | 0 | C | T | 47.4% | 100.4 / inf | 1074 | I168I (ATC→ATT) | yecD | isochorismatase family protein |
| Marginal new junction evidence (lowest skew 10 of 240 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207013 = | 508 (0.830) | 204 (0.400) | 110/168 | 4.8 | 34.1% | coding (290/630 nt) | stfP | e14 prophage; putative protein |
| ? | NC_000913 | 1208842 = | 362 (0.700) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; predicted side tail fiber protein fragment;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207028 | 528 (0.860) | 190 (0.370) | 108/168 | 5.2 | 32.6% | coding (305/630 nt) | stfP | e14 prophage; putative protein |
| ? | NC_000913 | = 1208825 | 344 (0.670) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; predicted side tail fiber protein fragment;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 173573 | NA (NA) | 185 (0.310) +TACG |
49/192 | 22.5 | 78.1% | noncoding (70/85 nt) | REP13 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP13 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 4294404 = | 54 (0.090) | noncoding (547/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | = 4540713 | 438 (0.710) | 53 (0.090) | 44/182 | 23.0 | 11.4% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4541009 | 428 (0.770) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4540705 = | 421 (0.690) | 41 (0.070) | 36/182 | 26.1 | 9.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4541019 = | 435 (0.780) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 1208841 | 444 (0.720) | 35 (0.070) | 22/170 | 31.1 | 7.0% | pseudogene (2/501 nt) | stfE | pseudogene, e14 prophage; predicted side tail fiber protein fragment;Phage or Prophage Related |
| ? | NC_000913 | 2469919 = | 558 (1.070) | pseudogene (226/579 nt) | yfdL | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 315236 | NA (NA) | 6 (0.010) | 6/190 | 44.2 | NA | noncoding (787/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315249 | NA (NA) | noncoding (800/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 314577 | NA (NA) | 7 (0.010) | 6/190 | 44.2 | NA | noncoding (128/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 314610 | NA (NA) | noncoding (161/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1555624 = | 555 (0.900) | 5 (0.010) | 5/182 | 44.3 | 1.00% | coding (439/927 nt) | ddpF | D,D‑dipeptide permease system, ATP‑binding component |
| ? | NC_000913 | 3714951 = | 488 (0.870) | coding (382/660 nt) | yiaD | multicopy suppressor of bamB; outer membrane lipoprotein | |||||
| * | ? | NC_000913 | 1858757 = | 556 (0.910) | 5 (0.010) | 5/184 | 44.5 | 1.1% | coding (600/1077 nt) | ydjL | putative oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| ? | NC_000913 | = 3141958 | 415 (0.740) | coding (229/1179 nt) | hybB | putative hydrogenase 2 cytochrome b type component | |||||