mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 39 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 5,536,163 | 0 | G | A | 48.9% | 370.2 / inf | 461 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 48.6% | 659.3 / inf | 733 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 114,794 | 0 | A | G | 42.4% | 1089.7 / inf | 840 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.4% | 518.1 / inf | 492 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 1,763,584 | 0 | T | G | 33.3% | 184.9 / 16.3 | 178 | W30G (TGG→GGG) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 32.9% | 355.7 / 47.9 | 301 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 32.7% | 305.1 / 22.6 | 178 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 32.0% | 1694.2 / inf | 769 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,039 | 0 | A | G | 31.9% | 882.1 / inf | 496 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 28.1% | 933.4 / inf | 465 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,590,213 | 0 | T | C | 27.3% | 1326.1 / inf | 535 | T254T (ACT→ACC) | PA14_RS21015 | site‑specific integrase |
| * | NC_008463 | 4,616,454 | 0 | T | G | 27.0% | 350.3 / 15.6 | 175 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 26.1% | 1254.8 / 98.5 | 475 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 6,224,310 | 0 | A | C | 25.8% | 1011.1 / 25.8 | 364 | intergenic (‑242/+19) | PA14_RS28445/PA14_RS28450 | secondary thiamine‑phosphate synthase enzyme YjbQ/ammonium transporter |
| * | NC_008463 | 5,910,256 | 0 | A | C | 25.5% | 696.3 / 22.1 | 298 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 4,347,580 | 0 | T | G | 25.1% | 834.6 / 24.2 | 404 | intergenic (‑79/+150) | PA14_RS19855/PA14_RS19860 | hypothetical protein/zonular occludens toxin family protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 25.0% | 661.2 / 65.8 | 303 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 4,497,770 | 0 | T | G | 24.9% | 1012.3 / 25.4 | 387 | F152V (TTC→GTC) | PA14_RS20540 | short chain dehydrogenase |
| * | NC_008463 | 3,563,334 | 0 | T | G | 24.5% | 440.6 / 21.7 | 276 | intergenic (‑407/‑355) | qscR/PA14_RS16205 | quorum‑sensing transcriptional repressor QscR/sterol desaturase family protein |
| * | NC_008463 | 1,763,540 | 0 | T | G | 24.4% | 414.1 / 13.3 | 300 | L15R (CTG→CGG) | PA14_RS08240 | RHS repeat protein |
| Marginal new junction evidence (lowest skew 10 of 374 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | 4591102 = | 428 (0.850) | 27 (0.080) | 22/208 | 21.8 | 9.9% | intergenic (+370/+1) | PA14_RS21015/PA14_RS21020 | site‑specific integrase/tRNA‑Lys |
| ? | NC_008463 | = 5251437 | 198 (0.570) | intergenic (+230/+2) | tpsA4/PA14_RS31290 | two‑partner secretion system exoprotein TpsA4/tRNA‑Lys | |||||
| * | ? | NC_008463 | = 473590 | 536 (1.060) | 27 (0.060) | 24/260 | 24.4 | 5.3% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 499 (1.140) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 5935541 | 567 (1.120) | 19 (0.040) | 17/258 | 27.5 | 3.8% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 471 (1.080) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 3395117 | 451 (0.890) | 17 (0.040) | 17/268 | 28.0 | 4.0% | coding (1131/1356 nt) | PA14_RS15470 | hypothetical protein |
| ? | NC_008463 | 3395557 = | 406 (0.900) | coding (157/261 nt) | yidD | membrane protein insertion efficiency factor YidD | |||||
| * | ? | NC_008463 | = 4972365 | 532 (1.050) | 11 (0.020) | 11/278 | 31.9 | 2.1% | coding (516/684 nt) | PA14_RS22730 | biotin/lipoate A/B protein ligase family protein |
| ? | NC_008463 | 4972846 = | 541 (1.150) | coding (35/684 nt) | PA14_RS22730 | biotin/lipoate A/B protein ligase family protein | |||||
| * | ? | NC_008463 | = 3341157 | 397 (0.780) | 10 (0.020) | 10/268 | 32.0 | 2.8% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 342 (0.760) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||
| * | ? | NC_008463 | = 2936004 | 363 (0.720) | 9 (0.020) | 8/244 | 32.0 | 2.9% | noncoding (88/1289 nt) | CRISPR | repeat region |
| ? | NC_008463 | 2936485 = | 318 (0.770) | noncoding (569/1289 nt) | CRISPR | repeat region | |||||
| * | ? | NC_008463 | = 44749 | 599 (1.180) | 10 (0.020) | 10/268 | 32.0 | 2.2% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 2855205 = | 356 (0.790) | coding (6638/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||
| * | ? | NC_008463 | = 44749 | 599 (1.180) | 10 (0.020) | 10/268 | 32.0 | 2.1% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 45182 = | 395 (0.870) | coding (2249/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 1664750 | 486 (0.960) | 10 (0.020) | 10/276 | 32.4 | 2.1% | coding (695/1716 nt) | PA14_RS07720 | MFS transporter |
| ? | NC_008463 | 1665216 = | 482 (1.040) | coding (229/1716 nt) | PA14_RS07720 | MFS transporter | |||||