mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC | 1,110 | +66 bp | intergenic (+1035/+2045) | TMARI_RS09660 → / ← TMARI_RS00005 | hypothetical protein/IGHMBP2 family helicase |
| RA | 8,781 | C→T | C558Y (TGT→TAT) | TMARI_RS00030 ← | NADH‑quinone oxidoreductase subunit NuoF |
| RA | 51,724 | G→A | L644L (CTC→CTT) | TMARI_RS00255 ← | xylan alpha‑1,2‑glucuronosidase |
| RA | 70,289 | G→A | D116N (GAT→AAT) | TMARI_RS00325 → | mannonate dehydratase |
| RA | 153,436 | C→T | intergenic (‑8/+10) | TMARI_RS00715 ← / ← TMARI_RS00720 | ribosome silencing factor/glutamine‑‑fructose‑6‑phosphate aminotransferase |
| RA | 174,525 | C→T | V182V (GTC→GTT) | TMARI_RS00820 → | leucine‑‑tRNA ligase |
| RA | 189,999 | C→T | noncoding (1033/1564 nt) | TMARI_RS00875 → | 16S ribosomal RNA |
| RA | 252,862 | C→T | G171G (GGG→GGA) | TMARI_RS01220 ← | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑LD‑ lysine ligase |
| RA | 253,934 | G→A | D165N (GAT→AAT) | TMARI_RS01225 → | hypothetical protein |
| RA | 254,907 | C→T | A295V (GCA→GTA) | TMARI_RS01230 → | glucose‑1‑phosphate adenylyltransferase subunit GlgD |
| RA | 255,452 | C→T | A102V (GCC→GTC) | TMARI_RS01235 → | glucose‑1‑phosphate adenylyltransferase |
| RA | 263,426 | C→T | A154V (GCG→GTG) | TMARI_RS01285 → | DNA‑protecting protein DprA |
| RA | 292,337 | C→T | P288S (CCT→TCT) | TMARI_RS01420 → | sugar ABC transporter substrate‑binding protein |
| RA | 323,757 | C→T | P242S (CCT→TCT) | TMARI_RS01555 → | ABC transporter ATP‑binding protein |
| RA | 324,273 | G→A | D92N (GAT→AAT) | TMARI_RS01560 → | endoglucanase |
| RA | 329,640 | C→T | R520K (AGA→AAA) | TMARI_RS01575 ← | alpha‑xylosidase |
| RA | 334,236 | C→T | L233L (CTC→CTT) | TMARI_RS01585 → | beta‑galactosidase |
| RA | 374,924 | C→T | S31N (AGC→AAC) | TMARI_RS01815 ← | TolC family protein |
| RA | 380,678 | C→T | F99F (TTC→TTT) | TMARI_RS01855 → | fibronectin‑binding domain‑containing protein |
| RA | 391,330 | C→T | R236R (AGG→AGA) | TMARI_RS01900 ← | AcrB/AcrD/AcrF family protein |
| RA | 423,580 | C→T | T29I (ACT→ATT) | TMARI_RS02045 → | P‑II family nitrogen regulator |
| RA | 441,508 | +G | coding (365/1095 nt) | gldA ← | glycerol dehydrogenase |
| RA | 453,685 | G→A | intergenic (‑55/‑192) | TMARI_RS02190 ← / → TMARI_RS02195 | carbohydrate ABC transporter substrate‑binding protein/pectate trisaccharide‑lyase |
| RA | 464,696 | C→T | H310H (CAC→CAT) | TMARI_RS02240 → | DUF2088 domain‑containing protein |
| RA | 529,260 | C→T | M94I (ATG→ATA) | TMARI_RS02570 ← | ABC transporter ATP‑binding protein |
| RA | 531,887 | Δ1 bp | intergenic (‑320/‑355) | TMARI_RS02580 ← / → TMARI_RS02585 | ABC transporter permease/molecular chaperone GroES |
| RA | 566,333 | G→A | V134M (GTG→ATG) | TMARI_RS02765 → | fumarate hydratase |
| RA | 596,931 | A→T | M26K (ATG→AAG) | TMARI_RS02905 ← | Rrf2 family transcriptional regulator |
| RA | 622,429 | C→T | T107M (ACG→ATG) | TMARI_RS03015 → | rod shape‑determining protein |
| RA | 653,212 | T→C | R25R (AGA→AGG) | TMARI_RS03175 ← | glycosyltransferase family 4 protein |
| RA | 692,396 | C→T | E232E (GAG→GAA) | TMARI_RS03390 ← | ribonuclease J |
| RA | 700,621 | C→T | P516S (CCC→TCC) | TMARI_RS03435 → | flagellar hook‑length control protein FliK |
| RA | 712,512 | (A)7→8 | coding (1061/1437 nt) | TMARI_RS03505 → | DNA polymerase III subunit gamma/tau |
| RA | 712,650 | +A | coding (1199/1437 nt) | TMARI_RS03505 → | DNA polymerase III subunit gamma/tau |
| RA | 725,314 | C→T | V283V (GTG→GTA) | TMARI_RS03590 ← | cinA‑like protein |
| RA | 732,714 | C→T | P79L (CCA→CTA) | TMARI_RS03625 → | MarR family transcriptional regulator |
| RA | 771,217 | C→T | D42N (GAT→AAT) | TMARI_RS03825 ← | tRNA (adenine‑N1)‑methyltransferase |
| RA | 775,454 | C→T | E144E (GAG→GAA) | TMARI_RS03850 ← | alpha‑glucosidase/alpha‑galactosidase |
| RA | 886,742 | C→T | D109N (GAC→AAC) | TMARI_RS04415 ← | glucose‑1‑phosphate thymidylyltransferase |
| RA | 927,801 | G→A | I15I (ATC→ATT) | TMARI_RS04645 ← | flagellar biosynthesis protein FlhA |
| RA | 961,214 | G→A | K317K (AAG→AAA) | TMARI_RS04830 → | hypothetical protein |
| RA | 1,008,986 | C→T | L738F (CTT→TTT) | TMARI_RS05055 → | DUF3883 domain‑containing protein |
| RA | 1,050,568 | C→T | G155G (GGG→GGA) | TMARI_RS05270 ← | mannose‑1‑phosphate guanylyltransferase |
| RA | 1,079,864 | C→T | G187S (GGT→AGT) | TMARI_RS05430 ← | ABC transporter permease |
| RA | 1,107,515 | G→A | R372K (AGA→AAA) | TMARI_RS05560 → | histidine‑‑tRNA ligase |
| RA | 1,162,954 | C→T | T180T (ACG→ACA) | TMARI_RS05860 ← | ABC transporter permease |
| RA | 1,187,604 | C→T | R24R (CGG→CGA) | TMARI_RS05970 ← | ABC transporter substrate‑binding protein |
| RA | 1,236,482 | G→A | G62R (GGA→AGA) | TMARI_RS06190 → | NADH dehydrogenase |
| RA | 1,250,396 | C→T | G427E (GGA→GAA) | TMARI_RS06255 ← | ABC transporter substrate‑binding protein |
| RA | 1,339,657 | G→A | G319D (GGT→GAT) | TMARI_RS06710 → | ABC transporter ATP‑binding protein |
| RA | 1,351,908 | A→G | A207A (GCT→GCC) | TMARI_RS06775 ← | hypothetical protein |
| RA | 1,446,537 | G→A | G127D (GGT→GAT) | TMARI_RS07295 → | glycerol kinase |
| RA | 1,468,583 | G→A | A195V (GCG→GTG) | TMARI_RS07400 ← | RNA polymerase sigma factor SigA |
| RA | 1,530,195 | T→G | L24R (CTC→CGC) | TMARI_RS07850 → | B12‑binding domain‑containing radical SAM protein |
| RA | 1,569,199 | C→A | S246Y (TCT→TAT) | TMARI_RS08065 → | peptide chain release factor 2 |
| RA | 1,645,038 | C→T | R111K (AGA→AAA) | TMARI_RS08475 ← | DNA‑binding response regulator |
| RA | 1,651,040 | G→A | S198S (TCC→TCT) | TMARI_RS08520 ← | class I SAM‑dependent methyltransferase |
| RA | 1,677,498 | G→A | M16I (ATG→ATA) | TMARI_RS08700 → | HD‑GYP domain‑containing protein |
| RA | 1,718,805 | G→A | R175K (AGA→AAA) | TMARI_RS08915 → | haloacid dehalogenase |
| RA | 1,755,576 | G→A | intergenic (‑37/+25) | TMARI_RS09105 ← / ← TMARI_RS09110 | ribosome maturation factor/tRNA‑Ser |
| RA | 1,784,731 | G→A | P265S (CCA→TCA) | TMARI_RS09265 ← | type III‑A CRISPR‑associated RAMP protein Csm4 |
| RA | 1,806,077 | G→A | H62Y (CAT→TAT) | TMARI_RS09375 ← | IS200/IS605 family transposase |
| MC JC | 1,814,273 | (CCCT)2→1 | intergenic (‑48/+60) | TMARI_RS09830 ← / ← TMARI_RS09405 | DUF4896 domain‑containing protein/maltose/maltodextrin ABC transporter substrate‑binding protein MalE |
| MC JC | 1,815,540 | Δ28 bp | intergenic (‑23/‑201) | TMARI_RS09405 ← / → TMARI_RS09410 | maltose/maltodextrin ABC transporter substrate‑binding protein MalE/alpha‑amylase |
| RA | 1,839,693 | G→A | G80R (GGA→AGA) | TMARI_RS09490 → | DUF4382 domain‑containing protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_021214 | 1341068–1341894 | 1351798–1350987 | 9094–10731 | 88 [81] | [85] 86 | [TMARI_RS06725]–[TMARI_RS06775] | [TMARI_RS06725], TMARI_RS06730, TMARI_RS06735, TMARI_RS06740, TMARI_RS09805, TMARI_RS06745, TMARI_RS06750, TMARI_RS06755, TMARI_RS06760, TMARI_RS06765, TMARI_RS06770, [TMARI_RS06775] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_021214 | 206152 = | 272 (0.970) | 135 (0.550) | 80/358 | 1.3 | 33.9% | noncoding (77/77 nt) | TMARI_RS00975 | tRNA‑Arg |
| ? | NC_021214 | = 206320 | 289 (1.170) | intergenic (‑11/+1) | TMARI_RS00980/TMARI_RS00985 | tRNA‑His/tRNA‑Arg | |||||