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 43 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 | 50.1% | 630.0 / inf | 766 | 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 | 45.6% | 376.7 / inf | 386 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 42.0% | 824.3 / inf | 808 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 2,040,287 | 0 | G | . | 37.9% | 947.9 / inf | 378 | coding (139/1017 nt) | PA14_RS09495 | glycosyltransferase family 4 protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 34.4% | 260.4 / 18.9 | 156 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.7% | 624.8 / inf | 537 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 33.3% | 282.4 / 19.9 | 154 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 33.2% | 830.9 / inf | 497 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 31.8% | 1357.0 / inf | 718 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,009 | 0 | A | G | 31.8% | 793.9 / inf | 431 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 30.7% | 543.1 / 71.6 | 282 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 29.6% | 256.1 / 48.9 | 152 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 27.4% | 582.9 / 44.0 | 280 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 4,829,315 | 0 | T | G | 27.2% | 955.3 / 112.3 | 382 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 6,352,993 | 0 | A | T | 26.3% | 864.6 / 67.8 | 377 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 26.2% | 422.3 / 14.9 | 275 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 2,954,003 | 0 | T | G | 26.1% | 886.1 / 46.9 | 389 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 6,206,227 | 0 | G | A | 25.8% | 128.8 / 57.2 | 66 | H128H (CAC→CAT) | PA14_RS28350 | Hcp family type VI secretion system effector |
| * | NC_008463 | 4,347,580 | 0 | T | G | 25.2% | 806.1 / 17.9 | 371 | intergenic (‑79/+150) | PA14_RS19855/PA14_RS19860 | hypothetical protein/zonular occludens toxin family protein |
| * | NC_008463 | 4,616,457 | 0 | C | G | 24.7% | 311.9 / 24.3 | 157 | intergenic (‑177/+25) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 339 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | 2586751 = | 355 (0.730) | 69 (0.150) | 52/278 | 19.1 | 17.2% | coding (427/1530 nt) | nuoM | NADH‑quinone oxidoreductase subunit M |
| ? | NC_008463 | = 2586747 | 332 (0.730) | coding (431/1530 nt) | nuoM | NADH‑quinone oxidoreductase subunit M | |||||
| * | ? | NC_008463 | = 3972146 | 10 (0.040) | 183 (0.390) +GGCTCG |
9/140 | 25.4 | 61.8% | coding (1449/2106 nt) | dnaX | DNA polymerase III subunit gamma/tau |
| ? | NC_008463 | 3972147 = | 216 (0.450) | coding (1448/2106 nt) | dnaX | DNA polymerase III subunit gamma/tau | |||||
| * | ? | NC_008463 | 902878 = | 502 (1.030) | 27 (0.060) | 25/276 | 28.4 | 5.5% | coding (26/423 nt) | hpaR | homoprotocatechuate degradation operon regulator HpaR |
| ? | NC_008463 | = 902871 | 464 (1.030) | coding (19/423 nt) | hpaR | homoprotocatechuate degradation operon regulator HpaR | |||||
| * | ? | NC_008463 | = 473590 | 563 (1.160) | 23 (0.050) | 22/258 | 28.5 | 4.4% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 501 (1.190) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 1530568 | 634 (1.310) | 16 (0.040) | 15/270 | 33.1 | 3.0% | coding (1099/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein |
| ? | NC_008463 | 1531091 = | 472 (1.070) | coding (1622/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 5935541 | 508 (1.050) | 14 (0.030) | 13/256 | 33.4 | 3.2% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 416 (1.000) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 3039478 | 530 (1.090) | 14 (0.030) | 12/272 | 35.1 | 2.6% | coding (153/561 nt) | msuE | FMN reductase |
| ? | NC_008463 | 3039851 = | 560 (1.270) | coding (526/561 nt) | msuE | FMN reductase | |||||
| * | ? | NC_008463 | = 3341157 | 489 (1.010) | 12 (0.030) | 11/266 | 35.4 | 2.8% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 407 (0.940) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||
| * | ? | NC_008463 | = 3304506 | 505 (1.040) | 12 (0.030) | 11/266 | 35.4 | 2.7% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 418 (0.970) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 3143295 | 442 (0.910) | 11 (0.030) | 11/266 | 35.4 | 2.5% | coding (731/783 nt) | PA14_RS14385 | TIM barrel protein |
| ? | NC_008463 | 3143692 = | 452 (1.040) | coding (334/783 nt) | PA14_RS14385 | TIM barrel protein | |||||