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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 2,597,759 | 1 | . | G | 67.2% | 1240.6 / inf | 454 | coding (187/1782 nt) | nuoC | NADH‑quinone oxidoreductase subunit C/D |
| * | NC_008463 | 6,206,069 | 0 | T | G | 57.6% | 289.5 / inf | 813 | 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 | 45.7% | 410.6 / inf | 435 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 38.2% | 1372.9 / inf | 848 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 35.5% | 522.0 / inf | 506 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 35.5% | 260.4 / 19.8 | 161 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 30.9% | 272.5 / 21.7 | 154 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 30.5% | 1738.4 / inf | 761 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,439 | 0 | C | G | 30.3% | 232.9 / 49.5 | 152 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 28.8% | 1076.6 / inf | 548 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 28.4% | 1007.7 / inf | 504 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 1,763,584 | 0 | T | G | 28.4% | 226.9 / 19.2 | 183 | W30G (TGG→GGG) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 5,125,799 | 0 | T | G | 26.9% | 308.5 / 32.2 | 217 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 5,910,256 | 0 | A | C | 26.4% | 747.2 / 45.6 | 309 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 1,763,534 | 0 | T | G | 26.1% | 439.8 / 36.8 | 309 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 867,378 | 0 | A | C | 25.7% | 847.4 / 28.7 | 410 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| * | NC_008463 | 3,515,876 | 0 | T | A | 25.7% | 658.0 / 82.2 | 309 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 1,443,205 | 0 | G | C | 24.7% | 665.7 / 56.2 | 284 | intergenic (‑117/+26) | PA14_RS06755/plsB | YbaY family lipoprotein/glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB |
| * | NC_008463 | 2,889,071 | 0 | A | C | 24.6% | 811.3 / 17.2 | 309 | intergenic (+77/‑66) | gcvP/PA14_RS13460 | aminomethyl‑transferring glycine dehydrogenase/serine hydroxymethyltransferase |
| * | NC_008463 | 4,829,315 | 0 | T | G | 24.6% | 986.3 / 78.1 | 400 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| Marginal new junction evidence (lowest skew 10 of 379 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 3722872 | 418 (0.800) | 31 (0.060) | 27/292 | 28.5 | 7.0% | coding (411/1527 nt) | PA14_RS16920 | inactive transglutaminase family protein |
| ? | NC_008463 | 3722884 = | 417 (0.820) | coding (423/1527 nt) | PA14_RS16920 | inactive transglutaminase family protein | |||||
| * | ? | NC_008463 | = 473590 | 649 (1.240) | 15 (0.030) | 15/260 | 32.3 | 2.7% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 518 (1.140) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 911595 | 609 (1.160) | 15 (0.030) | 15/270 | 33.0 | 2.8% | coding (100/807 nt) | hpaI | 4‑hydroxy‑2‑oxoheptanedioate aldolase |
| ? | NC_008463 | 912016 = | 507 (1.080) | coding (495/804 nt) | hpaH | 2‑oxo‑hepta‑3‑ene‑1,7‑dioic acid hydratase | |||||
| * | ? | NC_008463 | = 4523618 | 549 (1.050) | 14 (0.030) | 14/272 | 33.7 | 2.8% | coding (27/474 nt) | PA14_RS20680 | YchJ family protein |
| ? | NC_008463 | 4524021 = | 476 (1.000) | coding (430/474 nt) | PA14_RS20680 | YchJ family protein | |||||
| * | ? | NC_008463 | 5251438 = | 242 (0.460) | 7 (0.020) | 7/208 | 34.0 | 3.4% | intergenic (+231/+1) | tpsA4/PA14_RS31290 | two‑partner secretion system exoprotein TpsA4/tRNA‑Lys |
| ? | NC_008463 | = 5359391 | 228 (0.630) | intergenic (+367/+2) | PA14_RS24540/PA14_RS24545 | site‑specific integrase/tRNA‑Lys | |||||
| * | ? | NC_008463 | = 5935541 | 603 (1.150) | 15 (0.030) | 12/258 | 34.1 | 2.9% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 497 (1.110) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 229722 | 503 (0.960) | 14 (0.030) | 13/270 | 34.2 | 2.9% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 483 (1.030) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 1280408 | 475 (0.910) | 49 (0.090) | 15/296 | 34.6 | 9.2% | coding (264/396 nt) | PA14_RS06005 | DUF4345 domain‑containing protein |
| ? | NC_008463 | 1280715 = | 502 (0.970) | intergenic (‑44/+43) | PA14_RS06005/PA14_RS06010 | DUF4345 domain‑containing protein/M23 family metallopeptidase | |||||
| * | ? | NC_008463 | = 3304506 | 490 (0.940) | 12 (0.030) | 12/268 | 34.7 | 2.7% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 442 (0.950) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 585458 | 516 (0.990) | 12 (0.030) | 12/274 | 35.1 | 2.4% | coding (43/444 nt) | PA14_RS02680 | Lrp/AsnC family transcriptional regulator |
| ? | NC_008463 | 585955 = | 494 (1.030) | coding (63/525 nt) | PA14_RS02685 | Lrp/AsnC family transcriptional regulator | |||||