mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 63 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | TrimmedAssembly_T66_contig_7 | 137,491 | 0 | A | C | 64.4% | 595.7 / inf | 430 | noncoding (71/71 nt) | rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Gly‑TCC |
| * | TrimmedAssembly_T66_contig_9 | 101 | 0 | C | T | 53.2% | 50.6 / inf | 286 | intergenic (–/+158) | –/rasttk_feature_annotation_tool=elepa@bvbrc | –/hypothetical protein |
| * | TrimmedAssembly_T66_contig_41 | 279 | 0 | A | G | 47.4% | 78.1 / inf | 472 | K93E (AAA→GAA) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Mobile element protein |
| * | TrimmedAssembly_T66_contig_41 | 270 | 0 | A | C | 46.0% | 73.0 / inf | 439 | I90L (ATC→CTC) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Mobile element protein |
| * | TrimmedAssembly_T66_contig_41 | 287 | 0 | C | T | 45.6% | 169.7 / inf | 433 | T95T (ACC→ACT) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Mobile element protein |
| * | TrimmedAssembly_T66_contig_36 | 298 | 0 | A | G | 45.4% | 584.7 / inf | 1635 | S99S (TCA→TCG) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase |
| * | TrimmedAssembly_T66_contig_36 | 283 | 0 | G | A | 44.2% | 871.6 / inf | 1574 | V94V (GTG→GTA) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase |
| * | TrimmedAssembly_T66_contig_41 | 310 | 0 | G | A | 43.9% | 237.2 / inf | 449 | R103H (CGC→CAC) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Mobile element protein |
| * | TrimmedAssembly_T66_contig_36 | 347 | 0 | G | A | 43.5% | 843.1 / inf | 1473 | E116K (GAA→AAA) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase |
| * | TrimmedAssembly_T66_contig_36 | 682 | 0 | T | C | 42.1% | 741.6 / inf | 1223 | N227N (AAT→AAC) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase |
| * | TrimmedAssembly_T66_contig_36 | 703 | 0 | G | A | 41.4% | 1177.0 / inf | 1628 | K234K (AAG→AAA) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase |
| * | TrimmedAssembly_T66_contig_21 | 6,509 | 0 | A | G | 40.5% | 217.3 / inf | 284 | R54R (CGA→CGG) | rasttk_feature_annotation_tool=elepa@bvbrc | hypothetical protein |
| * | TrimmedAssembly_T66_contig_21 | 6,304 | 0 | T | C | 39.9% | 275.5 / inf | 264 | intergenic (+282/‑44) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/rasttk_feature_annotation_tool=elepa@bvbrc | Undecaprenyl‑phosphate galactosephosphotransferase (EC 2.7.8.6)/hypothetical protein |
| * | TrimmedAssembly_T66_contig_21 | 6,512 | 0 | G | A | 39.8% | 226.4 / inf | 262 | Q55Q (CAG→CAA) | rasttk_feature_annotation_tool=elepa@bvbrc | hypothetical protein |
| * | TrimmedAssembly_T66_contig_9 | 64 | 0 | G | A | 39.6% | 442.0 / inf | 499 | intergenic (–/+195) | –/rasttk_feature_annotation_tool=elepa@bvbrc | –/hypothetical protein |
| * | TrimmedAssembly_T66_contig_42 | 231 | 0 | A | G | 38.9% | 1128.6 / inf | 1350 | Y30H (TAT→CAT) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase, IS4 family |
| * | TrimmedAssembly_T66_contig_21 | 6,286 | 0 | C | T | 37.5% | 328.2 / 300.5 | 253 | intergenic (+264/‑62) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/rasttk_feature_annotation_tool=elepa@bvbrc | Undecaprenyl‑phosphate galactosephosphotransferase (EC 2.7.8.6)/hypothetical protein |
| * | TrimmedAssembly_T66_contig_21 | 6,279 | 0 | G | A | 35.5% | 362.9 / 281.5 | 252 | intergenic (+257/‑69) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/rasttk_feature_annotation_tool=elepa@bvbrc | Undecaprenyl‑phosphate galactosephosphotransferase (EC 2.7.8.6)/hypothetical protein |
| * | TrimmedAssembly_T66_contig_42 | 142 | 0 | A | G | 34.2% | 1768.5 / inf | 1406 | I59I (ATT→ATC) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase, IS4 family |
| * | TrimmedAssembly_T66_contig_10 | 69,375 | 0 | C | A | 33.3% | 372.0 / 40.9 | 185 | F76L (TTC→TTA) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Undecaprenyl‑phosphate galactosephosphotransferase (EC 2.7.8.6) |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | TrimmedAssembly_T66_contig_42 | = 76 | 653 (0.510) | 97 (0.080) | 33/256 | 0.9 | 13.1% | coding (243/318 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase, IS4 family |
| ? | TrimmedAssembly_T66_contig_42 | 81 = | 649 (0.510) | coding (238/318 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Transposase, IS4 family | |||||
| * | ? | TrimmedAssembly_T66_contig_10 | = 98898 | 0 (0.000) | 98 (0.390) | 36/260 | 3.2 | 52.7% | intergenic (+59/–) | rasttk_feature_annotation_tool=elepa@bvbrc/– | hypothetical protein/– |
| ? | TrimmedAssembly_T66_contig_2 | = 81 | 176 (0.570) | coding (80/180 nt) | rasttk_feature_annotation_tool=elepa@bvbrc | hypothetical protein | |||||
| * | ? | TrimmedAssembly_T66_contig_4 | 1 = | 0 (0.000) | 115 (0.520) | 35/258 | 3.9 | 71.9% | intergenic (–/+40) | –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | –/ABC transporter, permease protein (cluster 3, basic aa/glutamine/opines) |
| ? | TrimmedAssembly_T66_contig_6 | = 59 | 90 (0.430) | intergenic (–/+14) | –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | –/Pyruvate oxidase (EC 1.2.3.3) | |||||
| * | ? | TrimmedAssembly_T66_contig_10 | 1 = | 0 (0.000) | 38 (0.190) +27 bp |
21/206 | 4.7 | 95.1% | intergenic (–/‑419) | –/rasttk_feature_annotation_tool=elepa@bvbrc | –/hypothetical protein |
| ? | TrimmedAssembly_T66_contig_2 | 4 = | 5 (0.020) | coding (3/180 nt) | rasttk_feature_annotation_tool=elepa@bvbrc | hypothetical protein | |||||
| * | ? | TrimmedAssembly_T66_contig_12 | 287 = | 177 (0.960) | 60 (0.300) +ATT |
26/254 | 4.8 | 28.8% | intergenic (+4/‑1) | rasttk_feature_creation_tool=tRNAscan‑SE/rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Glu‑TTC/tRNA‑Val‑TAC |
| ? | TrimmedAssembly_T66_contig_4 | 245806 = | 126 (0.540) | intergenic (‑5/–) | rasttk_feature_creation_tool=tRNAscan‑SE/– | tRNA‑Asn‑GTT/– | |||||
| * | ? | TrimmedAssembly_T66_contig_10 | 1 = | 0 (0.000) | 65 (0.320) | 28/260 | 4.9 | 59.1% | intergenic (–/‑419) | –/rasttk_feature_annotation_tool=elepa@bvbrc | –/hypothetical protein |
| ? | TrimmedAssembly_T66_contig_6 | = 59 | 90 (0.430) | intergenic (–/+14) | –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | –/Pyruvate oxidase (EC 1.2.3.3) | |||||
| * | ? | TrimmedAssembly_T66_contig_6 | = 59 | 90 (0.430) | 84 (0.420) | 27/260 | 5.1 | 65.1% | intergenic (–/+14) | –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | –/Pyruvate oxidase (EC 1.2.3.3) |
| ? | TrimmedAssembly_T66_contig_8 | 1 = | 0 (0.000) | coding (78/78 nt) | rasttk_feature_annotation_tool=elepa@bvbrc | hypothetical protein | |||||
| * | ? | TrimmedAssembly_T66_contig_28 | = 3183 | 0 (0.000) | 121 (0.160) +41 bp |
41/178 | 5.2 | 100% | intergenic (‑135/–) | rasttk_feature_creation_tool=RNA_reps_LSU_rRNA/– | LSU rRNA ## 23S rRNA, large subunit ribosomal RNA/– |
| ? | TrimmedAssembly_T66_contig_32 | = 1640 | 0 (0.000) | intergenic (+24/–) | rasttk_feature_creation_tool=RNA_reps_SSU_rRNA/– | SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/– | |||||
| * | ? | TrimmedAssembly_T66_contig_20 | 39090 = | NA (NA) | 79 (0.420) +T |
27/258 | 5.2 | 100% | intergenic (+42/–) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– | L‑lactate dehydrogenase (EC 1.1.1.27)/– |
| ? | TrimmedAssembly_T66_contig_31 | = 1737 | 0 (0.000) | intergenic (‑386/–) | rasttk_feature_annotation_tool=elepa@bvbrc/– | hypothetical protein/– | |||||
| * | ? | TrimmedAssembly_T66_contig_16 | = 89249 | 0 (0.000) | 60 (0.230) | 23/260 | 7.0 | 40.5% | intergenic (+16/–) | rasttk_feature_annotation_tool=elepa@bvbrc/– | hypothetical protein/– |
| ? | TrimmedAssembly_T66_contig_2 | = 81 | 176 (0.570) | coding (80/180 nt) | rasttk_feature_annotation_tool=elepa@bvbrc | hypothetical protein | |||||