mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.38.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 36 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_010473 | 276,960 | 0 | C | T | 68.8% | 87.7 / 73.3 | 80 | E130K (GAG→AAG) | paoA | aldehyde dehydrogenase iron‑sulfur subunit PaoA |
| * | NC_010473 | 1,395,345 | 0 | A | G | 59.3% | 50.0 / 133.0 | 87 | E467G (GAA→GGA) | ECDH10B_RS07015 | Tn3‑like element ISEc63 family transposase |
| * | NC_010473 | 218,669 | 0 | T | A | 51.0% | 4.4 / 202.9 | 104 | L80Q (CTG→CAG) | yafJ | class II glutamine amidotransferase |
| * | NC_010473 | 4,658,888 | 0 | A | G | 38.5% | 56.2 / 40.0 | 39 | intergenic (+143/+277) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,834 | 0 | T | C | 37.5% | 61.2 / 36.0 | 41 | intergenic (+89/+331) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,880 | 0 | T | C | 37.5% | 58.0 / 34.3 | 41 | intergenic (+135/+285) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,820 | 0 | T | G | 36.6% | 69.4 / 54.2 | 41 | intergenic (+75/+345) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,828 | 0 | G | A | 36.6% | 69.1 / 38.2 | 41 | intergenic (+83/+337) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,829 | 0 | G | A | 36.6% | 67.9 / 36.8 | 41 | intergenic (+84/+336) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,908 | 0 | T | A | 35.7% | 67.8 / 56.0 | 42 | intergenic (+163/+257) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 4,658,921 | 0 | T | G | 34.2% | 68.9 / 48.7 | 41 | intergenic (+176/+244) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 1,455,375 | 0 | T | C | 33.9% | 87.7 / 60.3 | 66 | intergenic (‑43/‑124) | pspF/pspA | phage shock protein operon transcriptional activator/phage shock protein PspA |
| * | NC_010473 | 1,455,386 | 0 | T | C | 33.3% | 111.3 / 38.8 | 63 | intergenic (‑54/‑113) | pspF/pspA | phage shock protein operon transcriptional activator/phage shock protein PspA |
| * | NC_010473 | 4,658,907 | 0 | G | A | 33.3% | 67.0 / 49.8 | 42 | intergenic (+162/+258) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 1,455,383 | 0 | T | G | 32.8% | 113.1 / 61.3 | 62 | intergenic (‑51/‑116) | pspF/pspA | phage shock protein operon transcriptional activator/phage shock protein PspA |
| * | NC_010473 | 1,455,388 | 0 | T | A | 32.8% | 109.9 / 49.8 | 61 | intergenic (‑56/‑111) | pspF/pspA | phage shock protein operon transcriptional activator/phage shock protein PspA |
| * | NC_010473 | 4,658,935 | 0 | T | C | 32.5% | 63.6 / 34.3 | 40 | intergenic (+190/+230) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| * | NC_010473 | 1,455,380 | 0 | T | C | 31.2% | 111.3 / 58.3 | 64 | intergenic (‑48/‑119) | pspF/pspA | phage shock protein operon transcriptional activator/phage shock protein PspA |
| * | NC_010473 | 1,455,389 | 0 | T | A | 31.0% | 104.6 / 46.9 | 61 | intergenic (‑57/‑110) | pspF/pspA | phage shock protein operon transcriptional activator/phage shock protein PspA |
| * | NC_010473 | 4,658,941 | 0 | A | T | 30.8% | 64.6 / 43.3 | 40 | intergenic (+196/+224) | yjjV/yjjW | metal‑dependent hydrolase/YjjW family glycine radical enzyme activase |
| Marginal new junction evidence (lowest skew 10 of 462 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_010473 | 296335 = | 85 (2.220) | 23 (0.610) | 20/390 | 1.4 | 21.9% | intergenic (+480/‑47) | rclR/ykgE | reactive chlorine‑specific transcriptional regulator RclR/heterodisulfide reductase‑related iron‑sulfur binding cluster |
| ? | NC_010473 | = 296331 | 81 (2.160) | intergenic (+476/‑51) | rclR/ykgE | reactive chlorine‑specific transcriptional regulator RclR/heterodisulfide reductase‑related iron‑sulfur binding cluster | |||||
| * | ? | NC_010473 | = 1396295 | 66 (1.720) | 24 (0.640) | 19/392 | 1.6 | 27.1% | coding (2350/3009 nt) | ECDH10B_RS07015 | Tn3‑like element ISEc63 family transposase |
| ? | NC_010473 | 1396299 = | 64 (1.700) | coding (2354/3009 nt) | ECDH10B_RS07015 | Tn3‑like element ISEc63 family transposase | |||||
| * | ? | NC_010473 | = 320249 | NA (NA) | 19 (0.500) | 18/394 | 1.7 | NA | coding (29/914 nt) | ECDH10B_RS01625 | IS3‑like element IS2 family transposase |
| ? | NC_010473 | 320253 = | NA (NA) | coding (33/914 nt) | ECDH10B_RS01625 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_010473 | = 3838110 | 21 (0.550) | 17 (0.440) | 16/398 | 2.1 | 44.7% | coding (23/849 nt) | yiaJ | IclR family transcriptional regulator YiaJ |
| ? | NC_010473 | 3838114 = | 21 (0.550) | coding (19/849 nt) | yiaJ | IclR family transcriptional regulator YiaJ | |||||
| * | ? | NC_010473 | 1394899 = | 72 (1.880) | 15 (0.400) | 15/388 | 2.2 | 17.8% | coding (954/3009 nt) | ECDH10B_RS07015 | Tn3‑like element ISEc63 family transposase |
| ? | NC_010473 | = 1394894 | 68 (1.820) | coding (949/3009 nt) | ECDH10B_RS07015 | Tn3‑like element ISEc63 family transposase | |||||
| * | ? | NC_010473 | = 320649 | NA (NA) | 17 (0.450) | 15/396 | 2.3 | NA | coding (429/914 nt) | ECDH10B_RS01625 | IS3‑like element IS2 family transposase |
| ? | NC_010473 | 320653 = | NA (NA) | coding (433/914 nt) | ECDH10B_RS01625 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_010473 | = 15603 | NA (NA) | 15 (0.400) | 15/392 | 2.3 | NA | coding (159/1113 nt) | ECDH10B_RS00080 | IS4‑like element IS421 family transposase |
| ? | NC_010473 | 15607 = | NA (NA) | coding (163/1113 nt) | ECDH10B_RS00080 | IS4‑like element IS421 family transposase | |||||
| * | ? | NC_010473 | 305 = | 33 (0.860) | 14 (0.380) | 13/386 | 2.7 | 30.4% | intergenic (+50/‑32) | thrL/thrA | thr operon leader peptide/bifunctional aspartate kinase/homoserine dehydrogenase I |
| ? | NC_010473 | = 301 | 32 (0.860) | intergenic (+46/‑36) | thrL/thrA | thr operon leader peptide/bifunctional aspartate kinase/homoserine dehydrogenase I | |||||
| * | ? | NC_010473 | = 198544 | NA (NA) | 14 (0.370) | 13/396 | 2.8 | NA | noncoding (670/1542 nt) | ECDH10B_RS00915 | 16S ribosomal RNA |
| ? | NC_010473 | 198549 = | NA (NA) | noncoding (675/1542 nt) | ECDH10B_RS00915 | 16S ribosomal RNA | |||||
| * | ? | NC_010473 | 4604784 = | 29 (0.760) | 12 (0.320) | 12/388 | 2.9 | 30.3% | coding (896/1218 nt) | nanX | MFS transporter |
| ? | NC_010473 | = 4604780 | 27 (0.720) | coding (892/1218 nt) | nanX | MFS transporter | |||||