mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 21,644 | T→A | A34A (GCT→GCA) | CYL77_00125 → | bifunctional metallophosphatase/5'‑nucleotidase |
| RA | 32,227 | T→A | I184N (ATT→AAT) | CYL77_00185 → | ribose ABC transporter permease |
| MC JC | 39,987 | Δ1,732 bp | CYL77_00230 | CYL77_00230 | |
| RA | 83,756 | T→C | intergenic (+151/+93) | rrf → / ← CYL77_00445 | 5S ribosomal RNA/permease |
| RA | 153,864 | C→T | S181S (TCC→TCT) | CYL77_00770 → | permease |
| RA | 194,568 | Δ1 bp | intergenic (‑661/‑426) | CYL77_00975 ← / → CYL77_00980 | sugar porter family MFS transporter/IS30 family transposase ISCg2 |
| RA | 197,259 | G→A | M96I (ATG→ATA) | CYL77_00990 → | glutamate synthase large subunit |
| RA | 272,034 | C→T | T311I (ACC→ATC) | CYL77_01365 → | aspartate kinase |
| JC | 372,682 | Δ18 bp | coding (266‑283/1092 nt) | CYL77_01865 → | glycosyltransferase family 1 protein |
| RA | 408,479 | C→T | Y66Y (TAC→TAT) | CYL77_02015 → | hypothetical protein |
| RA | 421,428 | G→A | A21V (GCA→GTA) | CYL77_02075 ← | DUF2505 domain‑containing protein |
| RA | 510,597 | C→T | R399R (CGC→CGT) | CYL77_02525 → | NAD(P)/FAD‑dependent oxidoreductase |
| RA | 512,869 | 2 bp→TT | intergenic (+160/‑365) | CYL77_02540 → / → CYL77_02545 | 50S ribosomal protein L7/L12/DUF3068 domain‑containing protein |
| RA | 512,872 | G→C | intergenic (+163/‑363) | CYL77_02540 → / → CYL77_02545 | 50S ribosomal protein L7/L12/DUF3068 domain‑containing protein |
| RA | 536,027 | A→G | Q69R (CAG→CGG) | CYL77_02630 → | 50S ribosomal protein L4 |
| RA | 576,540 | A→C | K65T (AAG→ACG) | CYL77_02885 → | 30S ribosomal protein S4 |
| RA | 653,740 | C→T | D187D (GAC→GAT) | CYL77_03250 → | error‑prone DNA polymerase |
| JC | 669,874 | (GCCCGCTGTTTCT)1→2 | intergenic (‑372/‑47) | CYL77_03320 ← / → CYL77_03325 | O‑acetyl‑L‑homoserine sulfhydrolase/carbon starvation protein A |
| RA | 685,961 | G→C | Y232* (TAC→TAG) | CYL77_03395 ← | iron‑siderophore ABC transporter substrate‑binding protein |
| RA | 708,313 | C→T | P458S (CCG→TCG) | CYL77_03495 → | pyruvate carboxylase |
| RA | 947,066 | (T)6→7 | coding (306/1755 nt) | CYL77_04560 → | BCCT family transporter |
| RA | 1,244,414 | T→C | V59A (GTT→GCT) | CYL77_05985 → | homoserine dehydrogenase |
| RA | 1,324,992 | C→T | P290S (CCA→TCA) | CYL77_06355 → | iron‑siderophore ABC transporter substrate‑binding protein |
| RA | 1,366,595 | (G)7→8 | intergenic (‑26/+12) | CYL77_06550 ← / ← CYL77_06555 | TetR/AcrR family transcriptional regulator/hypothetical protein |
| MC JC | 1,401,669 | 12985 bp→19 bp | CYL77_06745–CYL77_06835 | 19 genes CYL77_06745, CYL77_06750, CYL77_06755, CYL77_06760, CYL77_06765, CYL77_06770, CYL77_06775, CYL77_06780, CYL77_06785, CYL77_06790, CYL77_06795, CYL77_06800, CYL77_06805, CYL77_06810, CYL77_06815, CYL77_06820, CYL77_06825, CYL77_06830, CYL77_06835 |
|
| RA | 1,611,226 | (C)7→8 | noncoding (80/85 nt) | CYL77_07745 → | tRNA‑Leu |
| MC JC | 1,611,960 | Δ612 bp | coding (1‑612/612 nt) | CYL77_07755 → | N‑acetyltransferase |
| MC JC | 1,638,596 | 4167 bp→20 bp | CYL77_07865–CYL77_07880 | CYL77_07865, CYL77_07870, CYL77_07875, CYL77_07880 | |
| RA | 1,691,401 | T→C | K35E (AAA→GAA) | CYL77_08075 ← | hypothetical protein |
| RA | 1,756,915 | (G)5→6 | pseudogene (288/557 nt) | CYL77_08370 ← | adenine phosphoribosyltransferase |
| RA | 1,759,261 | C→T | intergenic (‑454/+48) | CYL77_08375 ← / ← CYL77_08380 | peptide ABC transporter/protein translocase subunit SecF |
| MC JC | 1,778,276 | 221804 bp→20 bp | CYL77_08500–CYL77_09540 | 212 genes CYL77_08500, CYL77_08505, CYL77_08510, CYL77_08515, CYL77_08520, CYL77_08525, CYL77_08530, CYL77_08535, CYL77_08540, CYL77_08545, CYL77_08550, CYL77_08555, CYL77_08560, CYL77_08565, CYL77_08570, CYL77_08575, CYL77_08580, CYL77_08585, CYL77_08590, CYL77_08595, CYL77_08600, CYL77_08605, CYL77_08610, CYL77_08615, CYL77_08620, CYL77_08625, CYL77_08630, CYL77_08635, CYL77_08640, CYL77_08645, CYL77_08650, CYL77_08655, CYL77_08660, CYL77_08665, CYL77_08670, CYL77_08675, CYL77_08680, CYL77_08685, CYL77_08690, CYL77_08695, CYL77_08700, CYL77_08705, CYL77_08710, CYL77_08715, CYL77_08720, CYL77_08725, CYL77_08730, CYL77_08735, CYL77_08740, CYL77_08745, CYL77_08750, CYL77_08755, CYL77_08760, CYL77_08765, CYL77_08770, CYL77_08775, CYL77_08775, CYL77_08780, CYL77_08780, CYL77_08785, CYL77_08790, CYL77_08795, CYL77_08800, CYL77_08805, CYL77_08810, CYL77_08815, CYL77_08820, CYL77_08825, CYL77_08830, CYL77_08835, CYL77_08840, CYL77_08845, CYL77_08850, CYL77_08855, CYL77_08860, CYL77_08865, CYL77_08870, CYL77_08875, CYL77_08880, CYL77_08885, CYL77_08890, CYL77_08895, CYL77_08900, CYL77_08905, CYL77_08910, CYL77_08915, CYL77_08920, CYL77_08925, CYL77_08930, CYL77_08935, CYL77_08940, CYL77_08945, CYL77_08950, CYL77_08955, CYL77_08960, CYL77_08965, CYL77_08970, CYL77_08975, CYL77_08980, CYL77_08985, CYL77_08990, CYL77_08995, CYL77_09000, CYL77_09005, CYL77_09010, CYL77_09015, CYL77_09020, CYL77_09025, CYL77_09030, CYL77_09035, CYL77_09040, CYL77_09045, CYL77_09050, CYL77_09055, CYL77_09060, CYL77_09065, CYL77_09070, CYL77_09075, CYL77_09080, CYL77_09085, CYL77_09090, CYL77_09095, CYL77_09100, CYL77_09105, CYL77_09110, CYL77_09115, CYL77_09120, CYL77_09125, CYL77_09130, CYL77_09135, CYL77_09140, CYL77_09145, CYL77_09150, CYL77_09155, CYL77_09160, CYL77_09165, CYL77_09170, CYL77_09175, CYL77_09180, CYL77_09185, CYL77_09190, CYL77_09195, CYL77_09200, CYL77_09205, CYL77_09210, CYL77_09215, CYL77_09220, CYL77_09225, CYL77_09230, CYL77_09235, CYL77_09240, CYL77_09245, CYL77_09245, CYL77_09250, CYL77_09255, CYL77_09260, CYL77_09265, CYL77_09270, CYL77_09275, CYL77_09280, CYL77_09285, CYL77_09290, CYL77_09295, CYL77_09300, CYL77_09305, CYL77_09310, CYL77_09315, CYL77_09320, CYL77_09325, CYL77_09330, CYL77_09335, CYL77_09340, CYL77_09345, CYL77_09350, CYL77_09355, CYL77_09360, CYL77_09365, CYL77_09370, CYL77_09375, CYL77_09380, CYL77_09385, CYL77_09390, CYL77_09395, CYL77_09400, CYL77_09405, CYL77_09410, CYL77_09415, CYL77_09420, CYL77_09425, CYL77_09430, CYL77_09435, CYL77_09440, CYL77_09445, CYL77_09450, CYL77_09455, CYL77_09460, CYL77_09465, CYL77_09470, CYL77_09475, CYL77_09480, CYL77_09485, CYL77_09490, CYL77_09495, CYL77_09500, CYL77_09505, CYL77_09510, CYL77_09515, CYL77_09520, CYL77_09525, CYL77_09530, CYL77_09535, CYL77_09540 |
|
| RA | 2,033,966 | A→G | T159A (ACA→GCA) | CYL77_09715 → | LysR family transcriptional regulator |
| MC JC | 2,042,148 | 725 bp→20 bp | coding (19‑743/780 nt) | CYL77_09745 → | DeoR/GlpR transcriptional regulator |
| RA | 2,064,540 | T→C | L159P (CTT→CCT) | CYL77_09840 → | amino acid ABC transporter ATP‑binding protein |
| MC JC | 2,110,023 | Δ1,461 bp | CYL77_10055 | CYL77_10055 | |
| MC JC | 2,180,735 | (18-bp)3→2 | coding (529‑546/1749 nt) | CYL77_10385 ← | signal recognition particle‑docking protein FtsY |
| MC JC | 2,200,552 | 1289 bp→20 bp | coding (19‑1307/1344 nt) | CYL77_10460 ← | glutamate dehydrogenase |
| RA | 2,302,410 | (C)5→6 | pseudogene (265/389 nt) | CYL77_10905 ← | hypothetical protein |
| RA | 2,419,925 | A→G | Q194Q (CAA→CAG) | CYL77_11475 → | HNH endonuclease |
| RA | 2,441,706 | +T | pseudogene (909/2037 nt) | CYL77_11575 ← | peptidase |
| RA | 2,442,561 | Δ1 bp | pseudogene (54/2037 nt) | CYL77_11575 ← | peptidase |
| RA | 2,442,672 | Δ1 bp | pseudogene (26/1181 nt) | CYL77_11580 → | carboxylesterase/lipase family protein |
| RA | 2,442,735 | +A | pseudogene (89/1181 nt) | CYL77_11580 → | carboxylesterase/lipase family protein |
| RA | 2,442,991 | +C | pseudogene (345/1181 nt) | CYL77_11580 → | carboxylesterase/lipase family protein |
| RA | 2,443,054 | G→T | pseudogene (408/1181 nt) | CYL77_11580 → | carboxylesterase/lipase family protein |
| RA | 2,443,262 | +C | pseudogene (616/1181 nt) | CYL77_11580 → | carboxylesterase/lipase family protein |
| RA | 2,443,356 | Δ1 bp | pseudogene (710/1181 nt) | CYL77_11580 → | carboxylesterase/lipase family protein |
| RA | 2,551,504 | A→G | N146D (AAC→GAC) | benA → | benzoate 1,2‑dioxygenase large subunit |
| RA | 2,562,349 | (A)5→4 | intergenic (‑6/+94) | CYL77_12125 ← / ← CYL77_12130 | ATP‑dependent Clp protease proteolytic subunit/ISL3‑like element IS31831 family transposase |
| RA | 2,562,378 | +G | intergenic (‑35/+65) | CYL77_12125 ← / ← CYL77_12130 | ATP‑dependent Clp protease proteolytic subunit/ISL3‑like element IS31831 family transposase |
| MC JC | 2,562,422 | Δ1,459 bp | CYL77_12130 | CYL77_12130 | |
| RA | 2,563,935 | (A)6→7 | intergenic (‑183/+55) | CYL77_12130 ← / ← CYL77_12135 | ISL3‑like element IS31831 family transposase/trigger factor |
| RA | 2,565,278 | +A | pseudogene (61/1349 nt) | CYL77_12135 ← | trigger factor |
| RA | 2,565,429 | Δ1 bp | intergenic (‑91/+27) | CYL77_12135 ← / ← CYL77_12140 | trigger factor/tRNA‑Pro |
| RA | 2,566,259 | +G | pseudogene (418/497 nt) | CYL77_12145 → | ArsR family transcriptional regulator |
| RA | 2,730,982 | (C)7→6 | intergenic (+147/+9) | cysE → / ← CYL77_12975 | serine O‑acetyltransferase/N‑acetyltransferase |
| MC JC | 2,786,378 | Δ1,080 bp | coding (190‑1269/1485 nt) | CYL77_13235 → | MFS transporter |
| RA | 2,833,483 | C→T | V193I (GTT→ATT) | CYL77_13460 ← | LysE family translocator |
| RA | 2,978,635 | C→A | A132E (GCA→GAA) | CYL77_14095 → | flavin‑dependent oxidoreductase |
| MC JC | 3,059,619 | Δ1,069 bp | coding (429‑1497/1833 nt) | CYL77_14485 ← | phosphoenolpyruvate carboxykinase |
| RA | 3,085,070 | T→C | E309E (GAA→GAG) | CYL77_14560 ← | Terminal beta‑(1‑>2)‑arabinofuranosyltransferase |
| MC JC | 3,119,686 | 914 bp→20 bp | coding (16‑929/945 nt) | CYL77_14710 ← | L‑lactate dehydrogenase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP025533 | 78504–79986 | 83692–80047 | 62–5189 | 79 [78] | [78] 79 | [CYL77_00425]–rrf | [CYL77_00425],CYL77_00430,CYL77_00435,rrf |
| * | * | ÷ | CP025533 | 2593601 | 2594978 | 1378 | 79 [78] | [78] 79 | CYL77_12270 | HNH endonuclease |
| * | * | ÷ | CP025533 | 2710992–2711087 | 2719969 | 8883–8978 | 79 [78] | [77] 79 | [rrf]–rrf | [rrf],CYL77_12885,CYL77_12890,CYL77_12895,CYL77_12900,CYL77_12905,CYL77_12910,CYL77_12915,rrf |
| * | * | ÷ | CP025533 | 3153144–3156816 | 3158440–3156820 | 5–5297 | 79 [77] | [78] 79 | rrf–CYL77_14905 | rrf,CYL77_14895,CYL77_14900,CYL77_14905 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP025533 | 272376 = | 116 (0.910) | 124 (0.980) +CT |
110/492 | 0.1 | 50.9% | intergenic (+8/‑16) | CYL77_01365/CYL77_01370 | aspartate kinase/aspartate‑semialdehyde dehydrogenase |
| ? | CP025533 | 2085498 = | 125 (0.980) | intergenic (‑47/+5) | CYL77_09945/CYL77_09950 | thymidylate synthase (FAD)/4‑hydroxy‑tetrahydrodipicolinate reductase | |||||
| * | ? | CP025533 | = 273426 | 147 (1.160) | 125 (1.000) +GCTA |
111/488 | 0.0 | 48.7% | coding (1035/1035 nt) | CYL77_01370 | aspartate‑semialdehyde dehydrogenase |
| ? | CP025533 | 1241641 = | 121 (0.950) | coding (1636/1653 nt) | CYL77_05965 | arginine‑‑tRNA ligase | |||||
| * | ? | CP025533 | 612717 = | 2 (0.020) | 120 (0.950) | 106/496 | 0.1 | 98.4% | coding (327/1617 nt) | groL | molecular chaperone GroEL |
| ? | CP025533 | 2110023 = | NA (NA) | intergenic (+2/+13) | CYL77_10050/CYL77_10055 | ABC transporter ATP‑binding protein/ISL3 family transposase | |||||
| * | ? | CP025533 | = 612724 | 3 (0.020) | 111 (0.870) | 98/496 | 0.2 | 97.4% | coding (334/1617 nt) | groL | molecular chaperone GroEL |
| ? | CP025533 | = 2632710 | NA (NA) | intergenic (‑129/‑113) | CYL77_12475/CYL77_12480 | ISL3 family transposase/hypothetical protein | |||||
| * | ? | CP025533 | 1044913 = | 1 (0.010) | 137 (1.080) | 118/494 | 0.0 | 71.4% | intergenic (+336/+114) | CYL77_05015/CYL77_05020 | hypothetical protein/hypothetical protein |
| ? | CP025533 | 2793967 = | 109 (0.860) | intergenic (‑388/+10) | CYL77_13260/CYL77_13265 | LysR family transcriptional regulator/diaminopimelate dehydrogenase | |||||
| * | ? | CP025533 | = 1044917 | 1 (0.010) | 120 (0.950) +TT |
102/492 | 0.2 | 63.2% | intergenic (+340/+110) | CYL77_05015/CYL77_05020 | hypothetical protein/hypothetical protein |
| ? | CP025533 | = 2084621 | 140 (1.100) | intergenic (‑123/+78) | dapA/CYL77_09945 | 4‑hydroxy‑tetrahydrodipicolinate synthase/thymidylate synthase (FAD) | |||||
| * | ? | CP025533 | = 1243002 | 147 (1.160) | 146 (1.150) | 125/494 | 0.0 | 49.0% | intergenic (+4/+281) | lysA/CYL77_05975 | diaminopimelate decarboxylase/hypothetical protein |
| ? | CP025533 | = 2794955 | 157 (1.240) | intergenic (‑16/‑51) | CYL77_13265/CYL77_13270 | diaminopimelate dehydrogenase/polyhydroxybutyrate depolymerase | |||||
| * | ? | CP025533 | 1329802 = | 127 (1.000) | 131 (1.080) +GGATCCCCGATC |
107/472 | 0.0 | 53.1% | coding (910/1086 nt) | CYL77_06375 | oxidoreductase |
| ? | CP025533 | = 1330852 | 116 (0.910) | coding (106/873 nt) | CYL77_06385 | lysine export transcriptional regulatory protein LysG | |||||
| * | ? | CP025533 | 1732994 = | 1 (0.010) | 107 (0.840) | 97/496 | 0.3 | 65.4% | coding (273/1380 nt) | CYL77_08275 | replication‑associated recombination protein A |
| ? | CP025533 | 2515282 = | 112 (0.880) | intergenic (+1/+13) | CYL77_11900/CYL77_11905 | pirin/ISL3 family transposase | |||||
| * | ? | CP025533 | = 1733001 | 6 (0.050) | 139 (1.090) | 117/496 | 0.0 | 95.9% | coding (266/1380 nt) | CYL77_08275 | replication‑associated recombination protein A |
| ? | CP025533 | = 2563881 | NA (NA) | intergenic (‑129/+109) | CYL77_12130/CYL77_12135 | ISL3‑like element IS31831 family transposase/trigger factor | |||||
| * | ? | CP025533 | 2083588 = | 131 (1.030) | 109 (0.860) | 95/496 | 0.3 | 43.6% | coding (3/2157 nt) | CYL77_09935 | ribonuclease J |
| ? | CP025533 | = 2086260 | 151 (1.190) | intergenic (‑11/‑305) | CYL77_09950/CYL77_09955 | 4‑hydroxy‑tetrahydrodipicolinate reductase/hypothetical protein | |||||
| * | ? | CP025533 | 2110023 = | NA (NA) | 123 (0.970) | 103/496 | 0.1 | 97.6% | intergenic (+2/+13) | CYL77_10050/CYL77_10055 | ABC transporter ATP‑binding protein/ISL3 family transposase |
| ? | CP025533 | = 2702561 | 3 (0.020) | pseudogene (453/474 nt) | CYL77_12850 | IS630 family transposase | |||||
| * | ? | CP025533 | 2272423 = | 2 (0.020) | 135 (1.070) | 116/492 | 0.0 | 98.6% | coding (168/219 nt) | CYL77_10780 | hypothetical protein |
| ? | CP025533 | = 2353688 | NA (NA) | intergenic (‑421/+163) | CYL77_11120/CYL77_11125 | IS30 family transposase ISCg2/RDD family protein | |||||
| * | ? | CP025533 | = 2272427 | 2 (0.020) | 124 (0.980) | 104/496 | 0.1 | 98.4% | coding (172/219 nt) | CYL77_10780 | hypothetical protein |
| ? | CP025533 | 2352055 = | NA (NA) | intergenic (+229/+7) | CYL77_11115/CYL77_11120 | permease/IS30 family transposase ISCg2 | |||||
| * | ? | CP025533 | = 2632709 | NA (NA) | 121 (0.960) | 101/494 | 0.2 | 96.0% | intergenic (‑128/‑114) | CYL77_12475/CYL77_12480 | ISL3 family transposase/hypothetical protein |
| ? | CP025533 | 2702553 = | 5 (0.040) | pseudogene (461/474 nt) | CYL77_12850 | IS630 family transposase | |||||
| * | ? | CP025533 | 2702916 = | NA (NA) | 138 (1.090) | 121/494 | 0.0 | 96.5% | pseudogene (98/474 nt) | CYL77_12850 | IS630 family transposase |
| ? | CP025533 | 3286432 = | 5 (0.040) | coding (2392/4932 nt) | CYL77_15535 | damage‑inducible protein | |||||
| * | ? | CP025533 | = 2704601 | NA (NA) | 151 (1.190) | 127/494 | 0.0 | 99.3% | intergenic (+163/+2) | CYL77_12855/CYL77_12860 | IS1380 family transposase/DUF1648 domain‑containing protein |
| ? | CP025533 | = 3286438 | 1 (0.010) | coding (2386/4932 nt) | CYL77_15535 | damage‑inducible protein | |||||
| * | ? | CP025533 | 2728541 = | 3 (0.020) | 114 (0.900) | 104/494 | 0.1 | 97.5% | coding (271/297 nt) | CYL77_12960 | hypothetical protein |
| ? | CP025533 | = 3041096 | NA (NA) | intergenic (+6/‑309) | CYL77_14395/CYL77_14400 | IS30 family transposase ISCg2/YibE/F family protein | |||||
| * | ? | CP025533 | = 2728544 | 5 (0.040) | 115 (0.910) | 104/496 | 0.1 | 95.8% | coding (268/297 nt) | CYL77_12960 | hypothetical protein |
| ? | CP025533 | 3039462 = | NA (NA) | intergenic (+256/‑423) | CYL77_14390/CYL77_14395 | pyridoxal phosphate‑dependent aminotransferase/IS30 family transposase ISCg2 | |||||
| * | ? | CP025533 | 2751832 = | 1 (0.010) | 139 (1.090) | 114/496 | 0.0 | 99.3% | intergenic (+383/+270) | CYL77_13090/CYL77_13095 | DUF3073 domain‑containing protein/phosphoribosylformylglycinamidine cyclo‑ligase |
| ? | CP025533 | 3039462 = | NA (NA) | intergenic (+256/‑423) | CYL77_14390/CYL77_14395 | pyridoxal phosphate‑dependent aminotransferase/IS30 family transposase ISCg2 | |||||
| * | ? | CP025533 | = 2751834 | 1 (0.010) | 113 (0.890) | 97/496 | 0.3 | 99.1% | intergenic (+385/+268) | CYL77_13090/CYL77_13095 | DUF3073 domain‑containing protein/phosphoribosylformylglycinamidine cyclo‑ligase |
| ? | CP025533 | = 3041097 | NA (NA) | intergenic (+7/‑308) | CYL77_14395/CYL77_14400 | IS30 family transposase ISCg2/YibE/F family protein | |||||