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 54 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 3,976,191 | 1 | . | G | 58.1% | 1118.7 / inf | 483 | coding (34/378 nt) | PA14_RS18155 | hypothetical protein |
| * | NC_008463 | 5,536,163 | 0 | G | A | 48.1% | 358.7 / inf | 429 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 42.8% | 958.1 / inf | 760 | 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 | 39.2% | 1044.4 / inf | 860 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 1,763,584 | 0 | T | G | 34.8% | 202.4 / 17.6 | 178 | W30G (TGG→GGG) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.1% | 702.9 / inf | 558 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 32.4% | 878.2 / inf | 539 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 30.6% | 409.7 / 31.7 | 308 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 30.5% | 874.2 / inf | 494 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 30.4% | 627.0 / 83.8 | 309 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 114,865 | 0 | T | C | 30.2% | 1493.6 / inf | 730 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,910,256 | 0 | A | C | 30.1% | 576.7 / 42.7 | 295 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 4,347,580 | 0 | T | G | 29.2% | 725.4 / 25.5 | 365 | intergenic (‑79/+150) | PA14_RS19855/PA14_RS19860 | hypothetical protein/zonular occludens toxin family protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 27.9% | 1003.7 / 137.3 | 413 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 4,616,454 | 0 | T | G | 27.3% | 348.8 / 14.0 | 156 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 2,030,085 | 1 | . | G | 27.0% | 591.7 / inf | 319 | coding (785/1269 nt) | wecC | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| * | NC_008463 | 3,515,864 | 0 | T | A | 25.0% | 581.5 / 38.5 | 302 | intergenic (+618/+266) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 5,125,799 | 0 | T | G | 24.8% | 386.9 / 23.8 | 228 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 3,688,128 | 0 | T | G | 23.9% | 881.2 / 55.8 | 310 | V165G (GTC→GGC) | folD | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| * | NC_008463 | 5,460,283 | 0 | A | G | 23.9% | 1043.7 / 302.1 | 446 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 406 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 96548 | 22 (0.090) | 226 (0.470) +TGGCTG |
18/140 | 18.6 | 61.5% | 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 = | 252 (0.500) | 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 | = 704259 | 535 (1.060) | 24 (0.050) | 22/262 | 27.0 | 4.5% | coding (849/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein |
| ? | NC_008463 | 704746 = | 555 (1.250) | coding (1336/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein | |||||
| * | ? | NC_008463 | = 5935541 | 520 (1.030) | 19 (0.040) | 19/256 | 28.0 | 4.1% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 446 (1.030) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 3304506 | 421 (0.830) | 19 (0.040) | 18/266 | 29.1 | 4.9% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 367 (0.810) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 473590 | 662 (1.310) | 18 (0.040) | 17/258 | 29.2 | 3.2% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 530 (1.210) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | 5251438 = | 311 (0.610) | 11 (0.030) | 10/206 | 29.7 | 4.5% | intergenic (+231/+1) | tpsA4/PA14_RS31290 | two‑partner secretion system exoprotein TpsA4/tRNA‑Lys |
| ? | NC_008463 | = 5359391 | 250 (0.720) | intergenic (+367/+2) | PA14_RS24540/PA14_RS24545 | site‑specific integrase/tRNA‑Lys | |||||
| * | ? | NC_008463 | = 2377014 | 514 (1.010) | 15 (0.030) | 14/268 | 31.4 | 3.5% | coding (684/972 nt) | PA14_RS11075 | LysR family transcriptional regulator |
| ? | NC_008463 | 2377471 = | 373 (0.820) | coding (227/972 nt) | PA14_RS11075 | LysR family transcriptional regulator | |||||
| * | ? | NC_008463 | = 229722 | 521 (1.030) | 16 (0.040) | 14/268 | 31.4 | 3.2% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 504 (1.110) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 96553 | 433 (0.880) | 37 (0.080) +GTGGCG |
14/276 | 31.9 | 7.9% | pseudogene (81/723 nt) pseudogene (857/894 nt) |
tagH tagH |
type VI secretion system‑associated FHA domain protein TagH type VI secretion system‑associated FHA domain protein TagH |
| ? | NC_008463 | 96554 = | 451 (0.890) | pseudogene (80/723 nt) pseudogene (856/894 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 | = 46919 | NA (NA) | 12 (0.030) | 12/274 | 33.0 | 100% | coding (3986/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 47235 = | 0 (0.000) | coding (4302/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||