mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.28.1 revision 52323b585d6f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 289 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | DH1 | 4,320,650 | 0 | A | G | 62.7% | 543.9 / inf | 595 | R129G (AGA→GGA) | thiE | thiamine phosphate synthase |
| * | DH1 | 4,335,469 | 0 | A | G | 62.3% | 563.8 / inf | 626 | S41S (AGT→AGC) | rplA | 50S ribosomal protein L1 |
| * | DH1 | 4,338,643 | 0 | A | G | 60.6% | 544.7 / inf | 701 | noncoding (74/76 nt) | ECDH1_RS21430 | tRNA‑Thr |
| * | DH1 | 755,782 | 0 | T | C | 60.6% | 419.1 / inf | 589 | L14P (CTC→CCC) | glcD | FAD‑binding protein |
| * | DH1 | 3,184,649 | 0 | A | G | 59.8% | 174.5 / inf | 367 | noncoding (35/75 nt) | ECDH1_RS15800 | tRNA‑TERM |
| * | DH1 | 1,983,639 | 0 | G | A | 59.6% | 434.0 / inf | 545 | P12L (CCC→CTC) | pabB | aminodeoxychorismate synthase subunit I |
| * | DH1 | 2,102,378 | 0 | T | C | 59.5% | 352.3 / inf | 510 | K172E (AAA→GAA) | ydiF | hypothetical protein |
| * | DH1 | 1,537,810 | 0 | A | G | 59.5% | 357.4 / inf | 534 | N87D (AAC→GAC) | gyrA | DNA gyrase subunit A |
| * | DH1 | 4,078,681 | 0 | A | G | 59.5% | 323.1 / inf | 497 | pseudogene (1442/1959 nt) | cpdB | 2', 3'‑cyclic nucleotide 2'‑phosphodiesterase |
| * | DH1 | 1,743,558 | 0 | T | C | 59.5% | 371.5 / inf | 554 | V385V (GTT→GTC) | wzc | tyrosine‑protein kinase wzc |
| * | DH1 | 4,335,587 | 0 | A | G | 59.4% | 419.9 / inf | 609 | V2A (GTT→GCT) | rplA | 50S ribosomal protein L1 |
| * | DH1 | 2,424,486 | 0 | T | C | 59.4% | 357.4 / inf | 531 | intergenic (‑1/‑350) | paaA/paaZ | phenylacetate‑CoA oxygenase subunit PaaA/phenylacetic acid degradation bifunctional protein PaaZ |
| * | DH1 | 4,026,783 | 0 | A | G | 59.2% | 371.0 / inf | 568 | C269R (TGT→CGT) | lptF | LPS export ABC transporter permease LptF |
| * | DH1 | 2,709,903 | 0 | C | T | 59.2% | 387.5 / inf | 539 | P179L (CCG→CTG) | ldtC | peptidoglycan‑binding protein LysM |
| * | DH1 | 2,580,982 | 0 | T | C | 59.0% | 302.5 / inf | 469 | V209A (GTT→GCT) | adhE | bifunctional acetaldehyde‑CoA/alcohol dehydrogenase |
| * | DH1 | 4,235,982 | 0 | A | G | 59.0% | 358.8 / inf | 553 | S4P (TCA→CCA) | ghxP | permease |
| * | DH1 | 4,429,538 | 0 | A | C | 58.9% | 514.9 / inf | 526 | L85F (TTA→TTC) | fdoG | formate dehydrogenase‑N subunit alpha |
| * | DH1 | 4,289,987 | 0 | A | G | 58.8% | 321.2 / inf | 506 | F219S (TTC→TCC) | metH | methionine synthase |
| * | DH1 | 2,688,095 | 0 | A | G | 58.8% | 319.8 / inf | 502 | K115E (AAA→GAA) | purB | adenylosuccinate lyase |
| * | DH1 | 1,883,418 | 0 | C | T | 58.6% | 399.9 / inf | 581 | H24Y (CAC→TAC) | uvrC | excinuclease ABC subunit C |
| Marginal new junction evidence (lowest skew 10 of 63 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | DH1 | = 67831 | 256 (0.450) | 270 (0.510) | 168/280 | 3.3 | 51.1% | coding (619/717 nt) | rph | ribonuclease PH |
| ? | DH1 | 67915 = | 277 (0.520) | coding (703/717 nt) | rph | ribonuclease PH | |||||
| * | ? | DH1 | = 300335 | NA (NA) | 303 (0.530) | 173/300 | 4.2 | 54.0% | noncoding (772/773 nt) | repeat_region | repeat region |
| ? | DH1 | = 1971083 | 258 (0.450) | coding (41/210 nt) | cspC | cold‑shock protein CspC | |||||
| * | ? | DH1 | = 2201911 | 271 (0.480) | 250 (0.440) | 168/300 | 4.9 | 61.1% | coding (1337/1533 nt) | pntA | NAD(P) transhydrogenase subunit alpha |
| ? | DH1 | 2204947 = | 47 (0.080) | intergenic (‑382/‑30) | tqsA/mdtJ | AI‑2 transporter TqsA/spermidine export protein MdtJ | |||||
| * | ? | DH1 | = 300335 | NA (NA) | 239 (0.420) | 160/300 | 6.1 | 39.8% | noncoding (772/773 nt) | repeat_region | repeat region |
| ? | DH1 | 490607 = | 362 (0.640) | coding (3102/3801 nt) | yhdP | DUF3971 domain‑containing protein | |||||
| * | ? | DH1 | 299568 = | NA (NA) | 262 (0.460) | 157/300 | 6.6 | 41.5% | noncoding (5/773 nt) | repeat_region | repeat region |
| ? | DH1 | = 490615 | 369 (0.650) | coding (3110/3801 nt) | yhdP | DUF3971 domain‑containing protein | |||||
| * | ? | DH1 | 3203897 = | 372 (0.650) | 233 (0.430) | 147/284 | 6.7 | 39.8% | coding (512/708 nt) | ybeR | hypothetical protein |
| ? | DH1 | = 3203926 | 354 (0.660) | coding (483/708 nt) | ybeR | hypothetical protein | |||||
| * | ? | DH1 | = 2991630 | 309 (0.550) | 376 (0.670) | 152/298 | 7.2 | 54.9% | coding (331/1686 nt) | ybjL | transporter |
| ? | DH1 | = 3577068 | NA (NA) | noncoding (1198/1201 nt) | repeat_region | repeat region | |||||
| * | ? | DH1 | = 1971081 | 251 (0.450) | 285 (0.510) | 148/296 | 7.7 | 53.2% | coding (39/210 nt) | cspC | cold‑shock protein CspC |
| ? | DH1 | 3580751 = | NA (NA) | noncoding (1/976 nt) | repeat_region | repeat region | |||||
| * | ? | DH1 | 2991627 = | 334 (0.590) | 394 (0.690) | 150/300 | 7.8 | 54.1% | coding (328/1686 nt) | ybjL | transporter |
| ? | DH1 | 3575874 = | NA (NA) | noncoding (4/1201 nt) | repeat_region | repeat region | |||||
| * | ? | DH1 | = 4493676 | 321 (0.560) | 236 (0.410) | 149/300 | 8.0 | 42.6% | coding (569/1641 nt) | ubiB | ubiquinone biosynthesis protein UbiB |
| ? | DH1 | 4493689 = | 316 (0.560) | coding (556/1641 nt) | ubiB | ubiquinone biosynthesis protein UbiB | |||||