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 272,034 C→T T311I (ACC→ATC)  CYL77_01365 → aspartate kinase
MC 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_06745CYL77_06835 19 genes
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_07865CYL77_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_08500CYL77_09540 212 genes
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 2,593,620 +A pseudogene (176/1545 nt) CYL77_12270 → HNH endonuclease
RA 2,593,704 T→C pseudogene (260/1545 nt) CYL77_12270 → HNH endonuclease
RA 2,593,768 T→C pseudogene (324/1545 nt) CYL77_12270 → HNH endonuclease
RA 2,728,523 C→G V97L (GTC→CTC)  CYL77_12960 ← hypothetical protein
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 78500–79986 83715–80047 62–5216 111 [109] [110] 111 [CYL77_00425]–rrf [CYL77_00425],CYL77_00430,CYL77_00435,rrf
* * ÷ CP025533 2593849–2594806 2594996 191–1148 111 [110] [109] 112 [CYL77_12270] [CYL77_12270]
* * ÷ CP025533 2711033–2711087 2719949 8863–8917 111 [109] [110] 111 [rrf]–rrf [rrf],CYL77_12885,CYL77_12890,CYL77_12895,CYL77_12900,CYL77_12905,CYL77_12910,CYL77_12915,rrf
* * ÷ CP025533 3153150–3158494 3158494 1–5345 111 [110] [110] 111 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 =165 (0.980)145 (0.870)
+CT
120/492 0.3 47.8% intergenic (+8/‑16) CYL77_01365/CYL77_01370 aspartate kinase/aspartate‑semialdehyde dehydrogenase
?CP025533 2085498 = 154 (0.910)intergenic (‑47/+5) CYL77_09945/CYL77_09950 thymidylate synthase (FAD)/4‑hydroxy‑tetrahydrodipicolinate reductase
* ? CP025533 = 273426145 (0.860)174 (1.050)
+GCTA
143/488 0.0 53.4% coding (1035/1035 nt) CYL77_01370 aspartate‑semialdehyde dehydrogenase
?CP025533 1241641 = 164 (0.970)coding (1636/1653 nt) CYL77_05965 arginine‑‑tRNA ligase
* ? CP025533 612717 =2 (0.010)179 (1.060) 147/496 0.0 98.9% 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 = 6127249 (0.050)175 (1.040) 138/496 0.1 95.1% 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 =0 (0.000)171 (1.020) 148/494 0.0 66.4% intergenic (+336/+114) CYL77_05015/CYL77_05020 hypothetical protein/hypothetical protein
?CP025533 2793967 = 173 (1.030)intergenic (‑388/+10) CYL77_13260/CYL77_13265 LysR family transcriptional regulator/diaminopimelate dehydrogenase
* ? CP025533 = 10449171 (0.010)169 (1.010)
+TT
127/492 0.2 65.8% intergenic (+340/+110) CYL77_05015/CYL77_05020 hypothetical protein/hypothetical protein
?CP025533 = 2084621 176 (1.040)intergenic (‑123/+78) dapA/CYL77_09945 4‑hydroxy‑tetrahydrodipicolinate synthase/thymidylate synthase (FAD)
* ? CP025533 = 1243002170 (1.010)191 (1.140) 159/494 0.0 52.1% intergenic (+4/+281) lysA/CYL77_05975 diaminopimelate decarboxylase/hypothetical protein
?CP025533 = 2794955 182 (1.080)intergenic (‑16/‑51) CYL77_13265/CYL77_13270 diaminopimelate dehydrogenase/polyhydroxybutyrate depolymerase
* ? CP025533 1329802 =169 (1.000)172 (1.070)
+GGATCCCCGATC
143/472 0.0 53.5% coding (910/1086 nt) CYL77_06375 oxidoreductase
?CP025533 = 1330852 145 (0.860)coding (106/873 nt) CYL77_06385 lysine export transcriptional regulatory protein LysG
* ? CP025533 1732994 =11 (0.070)162 (0.960) 134/496 0.1 66.0% coding (273/1380 nt) CYL77_08275 replication‑associated recombination protein A
?CP025533 2515282 = 156 (0.920)intergenic (+1/+13) CYL77_11900/CYL77_11905 pirin/ISL3 family transposase
* ? CP025533 = 17330018 (0.050)158 (0.940) 126/496 0.2 95.2% 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 =165 (0.980)149 (0.880) 128/496 0.2 48.9% coding (3/2157 nt) CYL77_09935 ribonuclease J
?CP025533 = 2086260 146 (0.870)intergenic (‑11/‑305) CYL77_09950/CYL77_09955 4‑hydroxy‑tetrahydrodipicolinate reductase/hypothetical protein
* ? CP025533 2110023 =NA (NA)162 (0.960) 134/496 0.1 95.9% intergenic (+2/+13) CYL77_10050/CYL77_10055 ABC transporter ATP‑binding protein/ISL3 family transposase
?CP025533 = 2702561 7 (0.040)pseudogene (453/474 nt) CYL77_12850 IS630 family transposase
* ? CP025533 2272423 =2 (0.010)190 (1.140) 148/492 0.0 99.0% 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 = 22724272 (0.010)168 (1.000) 147/496 0.0 98.8% 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 = 2632709NA (NA)169 (1.010) 142/494 0.0 97.7% intergenic (‑128/‑114) CYL77_12475/CYL77_12480 ISL3 family transposase/hypothetical protein
?CP025533 2702553 = 4 (0.020)pseudogene (461/474 nt) CYL77_12850 IS630 family transposase
* ? CP025533 2702916 =NA (NA)165 (0.980) 136/494 0.1 96.0% pseudogene (98/474 nt) CYL77_12850 IS630 family transposase
?CP025533 3286432 = 7 (0.040)coding (2392/4932 nt) CYL77_15535 damage‑inducible protein
* ? CP025533 = 2704601NA (NA)172 (1.020) 143/494 0.0 98.9% intergenic (+163/+2) CYL77_12855/CYL77_12860 IS1380 family transposase/DUF1648 domain‑containing protein
?CP025533 = 3286438 2 (0.010)coding (2386/4932 nt) CYL77_15535 damage‑inducible protein
* ? CP025533 2751832 =0 (0.000)164 (0.970) 127/496 0.2 100% 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 = 27518342 (0.010)172 (1.020) 132/496 0.1 98.9% 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
* ? CP025533 2921785 =7 (0.040)178 (1.060) 153/496 0.0 96.2% coding (813/1671 nt) CYL77_13825 Na+/H+ antiporter subunit D
?CP025533 3039462 = NA (NA)intergenic (+256/‑423) CYL77_14390/CYL77_14395 pyridoxal phosphate‑dependent aminotransferase/IS30 family transposase ISCg2
* ? CP025533 = 29217872 (0.010)190 (1.130) 153/496 0.0 99.0% coding (815/1671 nt) CYL77_13825 Na+/H+ antiporter subunit D
?CP025533 = 3041097 NA (NA)intergenic (+7/‑308) CYL77_14395/CYL77_14400 IS30 family transposase ISCg2/YibE/F family protein