mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 1,403 | A→G | Y356C (TAC→TGC) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 450,073 | C→T | W190* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 822,421 | C→T | L26L (TTG→TTA) | ybhN ← | UPF0104 family inner membrane protein |
| RA | 933,022 | A→G | D143G (GAC→GGC) | lrp → | leucine‑responsive global transcriptional regulator |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,818,103 | A→T | V133E (GTA→GAA) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| JC JC | 2,492,323 | IS1 (–) +9 bp | coding (924‑932/1251 nt) | frc ← | formyl‑CoA transferase, NAD(P)‑binding |
| RA | 2,907,364 | A→T | L193Q (CTG→CAG) | eno ← | enolase |
| RA | 2,907,452 | C→G | V164L (GTT→CTT) | eno ← | enolase |
| RA | 3,060,146 | C→A | Q132K (CAG→AAG) | argP → | transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor |
| RA | 3,471,274 | C→A | G19V (GGC→GTC) | tufA ← | translation elongation factor EF‑Tu 1 |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| JC JC | 3,966,174 | IS1 (–) +9 bp | intergenic (+84/‑235) | trxA → / → rho | thioredoxin 1/transcription termination factor |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,430,521 | A→G | I220V (ATA→GTA) | cycA → | D‑alanine/D‑serine/glycine transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1896930 | 1898281 | 1352 | 4 [3] | [0] 11 | [sdaA] | [sdaA] |
| * | * | ÷ | NC_000913 | 2684277 | 2685525 | 1249 | 8 [0] | [3] 4 | [glyA] | [glyA] |
| * | * | ÷ | NC_000913 | 2929579 | 2930928 | 1350 | 12 [0] | [0] 8 | sdaB | L‑serine dehydratase 2 |
| * | * | ÷ | NC_000913 | 3258300 | 3259646 | 1347 | 6 [0] | [0] 10 | tdcG | L‑serine dehydratase 3, anaerobic |
| * | * | ÷ | NC_000913 | 3423799–3424234 | 3424507–3424239 | 6–709 | 4 [2] | [3] 4 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 228016 = | NA (NA) | 4 (0.140) | 4/284 | 2.4 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 381258 = | NA (NA) | 15 (0.510) | 7/296 | 1.7 | NA | pseudogene (3/417 nt) | yaiX | pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 6 (0.210) | 5/280 | 2.0 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 4 (0.140) | 4/280 | 2.3 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 398392 | 18 (0.600) | 5 (0.190) | 4/270 | 2.3 | 24.2% | coding (521/1095 nt) | yaiW | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein |
| ? | NC_000913 | = 398378 | 15 (0.560) | coding (507/1095 nt) | yaiW | microcin Bac7 uptake protein; outer membrane surface‑exposed lipoprotein | |||||
| * | ? | NC_000913 | 1207790 = | 2 (0.070) | 28 (1.050) | 20/266 | 0.2 | 92.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 3 (0.110) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 2 (0.070) | 24 (0.900) | 21/266 | 0.2 | 90.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 3 (0.110) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1615598 = | 34 (1.140) | 935 (32.700) | 148/286 | 0.0 | 97.6% | coding (795/882 nt) | yneJ | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 1625301 | 14 (0.490) | intergenic (+10/+34) | ydeJ/dcp | inactive PncC family protein/dipeptidyl carboxypeptidase II | |||||
| * | ? | NC_000913 | 2375202 = | 13 (0.440) | 6 (0.210) | 6/282 | 1.8 | 36.0% | coding (761/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase |
| ? | NC_000913 | 2375281 = | 9 (0.320) | coding (682/963 nt) | menC | O‑succinylbenzoyl‑CoA synthase | |||||
| * | ? | NC_000913 | = 2713829 | 29 (0.970) | 7 (0.250) | 6/276 | 1.8 | 20.9% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713908 | 26 (0.940) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 3299599 = | 15 (0.500) | 4 (0.140) | 4/278 | 2.3 | 22.2% | coding (317/444 nt) | yhbP | UPF0306 family protein |
| ? | NC_000913 | 3299641 = | 14 (0.500) | coding (275/444 nt) | yhbP | UPF0306 family protein | |||||
| * | ? | NC_000913 | = 3427065 | NA (NA) | 3 (0.110) | 3/280 | 2.7 | NA | intergenic (‑32/+11) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||