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 63 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 6,994 | 0 | A | C | 61.1% | 7.7 / 16.4 | 18 | G322G (GGT→GGG) | yaaJ | sodium:alanine symporter family protein |
| * | NZ_CP009273 | 56,379 | 0 | T | G | 57.6% | 25.4 / 42.0 | 33 | Y244S (TAC→TCC) | lptD | LPS assembly protein LptD |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 57.1% | ‑4.9 / 22.2 | 21 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 2,621,984 | 0 | A | C | 57.1% | 7.4 / 20.6 | 21 | V105G (GTC→GGC) | pdeF | cyclic‑guanylate‑specific phosphodiesterase PdeF |
| * | NZ_CP009273 | 859,169 | 0 | T | G | 56.2% | 8.4 / 12.0 | 16 | G24G (GGT→GGG) | fsa | fructose‑6‑phosphate aldolase |
| * | NZ_CP009273 | 1,508,252 | 0 | A | G | 56.2% | ‑0.6 / 15.9 | 16 | G55G (GGA→GGG) | ydcU | ABC transporter permease |
| * | NZ_CP009273 | 760,187 | 0 | G | C | 55.6% | 7.9 / 26.0 | 18 | P184P (CCG→CCC) | sucD | succinate‑‑CoA ligase subunit alpha |
| * | NZ_CP009273 | 1,182,430 | 0 | C | A | 55.6% | 3.9 / 10.6 | 9 | N377K (AAC→AAA) | pepT | peptidase T |
| * | NZ_CP009273 | 3,138,764 | 0 | A | T | 55.6% | 6.2 / 34.8 | 27 | V286E (GTG→GAG) | hybO | hydrogenase 2 small subunit |
| * | NZ_CP009273 | 642,666 | 0 | A | C | 55.0% | 8.8 / 22.0 | 20 | G100G (GGT→GGG) | citG | triphosphoribosyl‑dephospho‑CoA synthase CitG |
| * | NZ_CP009273 | 982,470 | 0 | A | C | 54.5% | 7.1 / 11.2 | 11 | intergenic (‑32/+571) | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
| * | NZ_CP009273 | 1,872,730 | 0 | C | G | 54.2% | 2.5 / 37.3 | 24 | G253G (GGC→GGG) | dgcP | diguanylate cyclase DgcP |
| * | NZ_CP009273 | 1,673,544 | 0 | G | A | 53.8% | 18.6 / 32.7 | 26 | K287K (AAG→AAA) ‡ | ydgH | DUF1471 family protein YdgH |
| * | NZ_CP009273 | 2,380,362 | 0 | C | T | 53.8% | ‑0.3 / 13.8 | 13 | intergenic (+52/‑51) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 4,058,958 | 0 | G | A | 53.8% | 10.9 / 30.3 | 26 | L57L (CTG→TTG) | yihO | MFS transporter |
| * | NZ_CP009273 | 766,368 | 0 | A | T | 53.3% | 3.7 / 15.0 | 15 | intergenic (+301/‑546) | mngB/cydA | mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I |
| * | NZ_CP009273 | 2,002,571 | 0 | A | G | 53.3% | 5.7 / 12.9 | 15 | I272V (ATC→GTC) | yedE | selenium metabolism membrane protein YedE/FdhT |
| * | NZ_CP009273 | 108,789 | 0 | T | C | 52.9% | 7.4 / 16.6 | 17 | S100G (AGC→GGC) | zapD | cell division protein ZapD |
| * | NZ_CP009273 | 822,955 | 0 | T | G | 52.6% | 13.7 / 23.7 | 19 | T495P (ACC→CCC) | ybhF | ATP‑binding cassette domain‑containing protein |
| * | NZ_CP009273 | 1,548,257 | 0 | T | G | 52.6% | 11.5 / 18.6 | 19 | Y557S (TAC→TCC) | maeA | malate dehydrogenase |
| 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 | = 4195934 | 21 (0.660) | 3 (0.110) | 3/146 | 2.4 | 12.2% | coding (1527/1590 nt) | purH | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase |
| ? | NZ_CP009273 | 4196004 = | 25 (0.900) | coding (1457/1590 nt) | purH | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase | |||||
| * | ? | NZ_CP009273 | 4049856 = | 33 (1.040) | 3 (0.110) | 3/148 | 2.4 | 10.0% | intergenic (‑157/+129) | glnL/glnA | nitrogen regulation protein NR(II)/glutamate‑‑ammonia ligase |
| ? | NZ_CP009273 | 4049890 = | 25 (0.890) | intergenic (‑191/+95) | glnL/glnA | nitrogen regulation protein NR(II)/glutamate‑‑ammonia ligase | |||||
| * | ? | NZ_CP009273 | 4532499 = | 14 (0.440) | 3 (0.110) | 3/150 | 2.5 | 13.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 26 (0.920) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 3454958 = | 44 (1.380) | 3 (0.100) | 3/152 | 2.5 | 7.1% | coding (132/510 nt) | gspH | type II secretion system minor pseudopilin GspH |
| ? | NZ_CP009273 | 3455001 = | 39 (1.350) | coding (175/510 nt) | gspH | type II secretion system minor pseudopilin GspH | |||||
| * | ? | NZ_CP009273 | 3440178 = | 30 (0.940) | 3 (0.110) | 3/150 | 2.5 | 8.6% | coding (66/306 nt) | rpsN | 30S ribosomal protein S14 |
| ? | NZ_CP009273 | 3440220 = | 37 (1.300) | coding (24/306 nt) | rpsN | 30S ribosomal protein S14 | |||||
| * | ? | NZ_CP009273 | 619757 = | 53 (1.670) | 3 (0.110) | 3/150 | 2.5 | 6.6% | coding (210/957 nt) | fepB | Fe2+‑enterobactin ABC transporter substrate‑binding protein |
| ? | NZ_CP009273 | 619788 = | 37 (1.300) | coding (179/957 nt) | fepB | Fe2+‑enterobactin ABC transporter substrate‑binding protein | |||||
| * | ? | NZ_CP009273 | 391213 = | 28 (0.880) | 3 (0.110) | 3/150 | 2.5 | 13.3% | coding (531/1158 nt) | ampH | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase AmpH |
| ? | NZ_CP009273 | 391301 = | 14 (0.490) | coding (443/1158 nt) | ampH | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase AmpH | |||||