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 49 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 6,206,069 | 0 | T | G | 51.0% | 507.5 / inf | 676 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 5,536,163 | 0 | G | A | 49.1% | 271.7 / inf | 342 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 37.6% | 1240.0 / inf | 750 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,454 | 0 | T | G | 36.3% | 383.5 / 43.0 | 232 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 34.8% | 343.5 / 30.6 | 227 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 34.6% | 563.8 / inf | 519 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 33.7% | 933.0 / inf | 551 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 32.1% | 864.4 / inf | 496 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 31.0% | 532.0 / 78.8 | 283 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 114,865 | 0 | T | C | 29.4% | 1630.4 / inf | 688 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,448 | 0 | G | C | 29.0% | 399.0 / 60.9 | 227 | intergenic (‑168/+34) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 27.8% | 680.4 / 32.0 | 301 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 5,248,950 | 0 | T | G | 27.6% | 1189.2 / 40.8 | 494 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 1,763,534 | 0 | T | G | 27.0% | 396.0 / 26.0 | 270 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 27.0% | 340.5 / 66.2 | 215 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 3,325,906 | 0 | A | C | 26.8% | 810.2 / 40.6 | 305 | L41V (TTG→GTG) | PA14_RS15205 | SDR family oxidoreductase |
| * | NC_008463 | 5,125,799 | 0 | T | G | 26.4% | 368.3 / 34.5 | 262 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 6,352,993 | 0 | A | T | 25.9% | 906.1 / 65.8 | 381 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_008463 | 4,590,213 | 0 | T | C | 25.9% | 1547.0 / inf | 612 | T254T (ACT→ACC) | PA14_RS21015 | site‑specific integrase |
| * | NC_008463 | 2,889,071 | 0 | A | C | 25.3% | 682.7 / 22.3 | 260 | intergenic (+77/‑66) | gcvP/PA14_RS13460 | aminomethyl‑transferring glycine dehydrogenase/serine hydroxymethyltransferase |
| Marginal new junction evidence (lowest skew 10 of 220 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | 4591102 = | 461 (0.940) | 39 (0.120) | 30/208 | 17.2 | 12.3% | intergenic (+370/+1) | PA14_RS21015/PA14_RS21020 | site‑specific integrase/tRNA‑Lys |
| ? | NC_008463 | = 5251437 | 238 (0.700) | intergenic (+230/+2) | tpsA4/PA14_RS31290 | two‑partner secretion system exoprotein TpsA4/tRNA‑Lys | |||||
| * | ? | NC_008463 | = 5251483 | 365 (0.750) | 21 (0.060) | 19/208 | 21.5 | 7.8% | noncoding (78/122 nt) | PA14_RS31290 | tRNA‑Lys |
| ? | NC_008463 | 5359438 = | 247 (0.730) | noncoding (31/76 nt) | PA14_RS24545 | tRNA‑Lys | |||||
| * | ? | NC_008463 | = 4591147 | 459 (0.940) | 24 (0.070) | 19/208 | 21.5 | 7.9% | noncoding (32/76 nt) | PA14_RS21020 | tRNA‑Lys |
| ? | NC_008463 | 5251484 = | 242 (0.720) | noncoding (77/122 nt) | PA14_RS31290 | tRNA‑Lys | |||||
| * | ? | NC_008463 | = 96548 | 13 (0.050) | 216 (0.460) +TGGCTG |
7/142 | 23.1 | 62.8% | pseudogene (86/723 nt) pseudogene (862/894 nt) |
tagH tagH |
type VI secretion system‑associated FHA domain protein TagH type VI secretion system‑associated FHA domain protein TagH |
| ? | NC_008463 | 96549 = | 241 (0.490) | pseudogene (85/723 nt) pseudogene (861/894 nt) |
tagH tagH |
type VI secretion system‑associated FHA domain protein TagH type VI secretion system‑associated FHA domain protein TagH |
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| * | ? | NC_008463 | = 473590 | 614 (1.260) | 16 (0.040) | 16/260 | 26.2 | 3.1% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 482 (1.140) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 3595112 | 362 (0.740) | 16 (0.040) | 15/256 | 26.4 | 5.0% | coding (1603/8145 nt) | PA14_RS16325 | Ig‑like domain‑containing protein |
| ? | NC_008463 | 3595359 = | 304 (0.730) | coding (1356/8145 nt) | PA14_RS16325 | Ig‑like domain‑containing protein | |||||
| * | ? | NC_008463 | = 5935541 | 525 (1.070) | 16 (0.040) | 13/258 | 27.6 | 3.5% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 434 (1.030) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | 2982872 = | 414 (0.850) | 14 (0.030) | 13/298 | 29.6 | 3.1% | coding (4224/7347 nt) | pvdD | pyoverdine non‑ribosomal peptide synthetase PvdD |
| ? | NC_008463 | = 2991691 | 458 (0.940) | coding (796/855 nt) | PA14_RS13740 | formylglycine‑generating enzyme family protein | |||||
| * | ? | NC_008463 | = 100189 | 560 (1.140) | 9 (0.020) | 9/268 | 30.5 | 1.9% | coding (759/1497 nt) | tssC | type VI secretion system contractile sheath large subunit |
| ? | NC_008463 | 100610 = | 448 (1.030) | coding (1180/1497 nt) | tssC | type VI secretion system contractile sheath large subunit | |||||
| * | ? | NC_008463 | = 2936784 | 467 (0.950) | 7 (0.020) | 6/244 | 31.4 | 1.9% | noncoding (868/1289 nt) | CRISPR | repeat region |
| ? | NC_008463 | 2937206 = | 331 (0.830) | intergenic (‑1550/+270) | cas1f/PA14_RS13605 | type I‑F CRISPR‑associated endonuclease Cas1f/hypothetical protein | |||||