breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence seq id position mutation annotation gene description
JC Annotation_U21_Trimmed_contig_1 47 +84 bp coding (47/567 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 → hypothetical protein
RA Annotation_U21_Trimmed_contig_1 64,267 T→C S371P (TCA→CCA)  rasttk_feature_annotation_tool=annotate_proteins_km er_v2 → RNA polymerase sigma factor RpoD
RA Annotation_U21_Trimmed_contig_4 75,126 T→C C31R (TGC→CGC)  rasttk_feature_annotation_tool=annotate_proteins_km er_v2 → Replication‑associated recombination protein RarA
JC Annotation_U21_Trimmed_contig_8 16 +84 bp coding (573/588 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 ← hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ Annotation_U21_Trimmed_contig_3 1 1 1 NA [0] [0] 1613 –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 –/Integral membrane protein LafC, accessory function in glycolipid and LTA synthesis
* * ÷ Annotation_U21_Trimmed_contig_9 10580–10601 10661 61–82 1185 [1151] [0] NA rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– ORF9/–

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? Annotation_U21_Trimmed_contig_1 1 =0 (0.000)151 (0.560) 57/256 1.7 100% coding (1/567 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 hypothetical protein
?Annotation_U21_Trimmed_contig_8 1 = 0 (0.000)coding (588/588 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 hypothetical protein
* ? Annotation_U21_Trimmed_contig_1 = 5087 (0.320)37 (0.930)
+109 bp		 7/38 1.1 69.5% coding (50/567 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 hypothetical protein
?Annotation_U21_Trimmed_contig_1 76 = 132 (0.490)coding (76/567 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 hypothetical protein
* ? Annotation_U21_Trimmed_contig_10 1 =0 (0.000)450 (0.470)
+GTTTATTCCGGCA		 62/230 0.5 84.4% noncoding (117/117 nt) rasttk_feature_creation_tool=RNA_reps_5S_rRNA 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation
?Annotation_U21_Trimmed_contig_12 = 910 185 (0.680)noncoding (8/73 nt) rasttk_feature_creation_tool=tRNAscan‑SE tRNA‑Lys‑TTT
* ? Annotation_U21_Trimmed_contig_10 1 =0 (0.000)337 (0.310) 96/256 0.0 100% noncoding (117/117 nt) rasttk_feature_creation_tool=RNA_reps_5S_rRNA 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation
?Annotation_U21_Trimmed_contig_12 = 1004 0 (0.000)intergenic (‑5/–) rasttk_feature_creation_tool=tRNAscan‑SE/– tRNA‑Val‑TAC/–
* ? Annotation_U21_Trimmed_contig_10 1 =0 (0.000)353 (0.500)
+46 bp		 70/164 0.0 100% noncoding (117/117 nt) rasttk_feature_creation_tool=RNA_reps_5S_rRNA 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation
?Annotation_U21_Trimmed_contig_3 = 367983 0 (0.000)intergenic (‑70/–) rasttk_feature_creation_tool=tRNAscan‑SE/– tRNA‑Thr‑GGT/–
* ? Annotation_U21_Trimmed_contig_10 1 =0 (0.000)342 (0.460)
+46 bp		 69/164 0.1 100% noncoding (117/117 nt) rasttk_feature_creation_tool=RNA_reps_5S_rRNA 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation
?Annotation_U21_Trimmed_contig_5 = 139689 0 (0.000)intergenic (+108/–) rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– Uncharacterized deacetylase/–
* ? Annotation_U21_Trimmed_contig_10 = 32970 (0.000)986 (0.580)
+TTGAGAGTAA		 113/236 1.4 100% intergenic (‑160/–) rasttk_feature_creation_tool=RNA_reps_LSU_rRNA/– LSU rRNA ## 23S rRNA, large subunit ribosomal RNA/–
?Annotation_U21_Trimmed_contig_11 = 1711 0 (0.000)intergenic (+53/–) rasttk_feature_creation_tool=RNA_reps_SSU_rRNA/– SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/–
* ? Annotation_U21_Trimmed_contig_11 1 =0 (0.000)1612 (1.490)
+C		 130/254 0.0 100% intergenic (–/‑74) –/rasttk_feature_creation_tool=RNA_reps_SSU_rRNA –/SSU rRNA ## 16S rRNA, small subunit ribosomal RNA
?Annotation_U21_Trimmed_contig_3 2 = 0 (0.000)intergenic (–/+370) –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 –/Integral membrane protein LafC, accessory function in glycolipid and LTA synthesis
* ? Annotation_U21_Trimmed_contig_11 = 17110 (0.000)356 (0.400)
+22 bp		 67/212 0.0 73.6% intergenic (+53/–) rasttk_feature_creation_tool=RNA_reps_SSU_rRNA/– SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/–
?Annotation_U21_Trimmed_contig_13 191 = 309 (0.980)noncoding (1/75 nt) rasttk_feature_creation_tool=tRNAscan‑SE tRNA‑Ile‑GAT
* ? Annotation_U21_Trimmed_contig_13 1 =0 (0.000)162 (0.550) 49/256 1.5 58.3% intergenic (–/‑4) –/rasttk_feature_creation_tool=tRNAscan‑SE –/tRNA‑Phe‑GAA
?Annotation_U21_Trimmed_contig_8 48167 = 232 (0.860)intergenic (‑22/+1) rasttk_feature_creation_tool=tRNAscan‑SE/rasttk_feature_creation_tool=tRNAscan‑SE tRNA‑Phe‑GAA/tRNA‑Asp‑GTC
* ? Annotation_U21_Trimmed_contig_2 = 374547465 (1.060)487 (1.090) 82/252 0.7 68.0% coding (3920/5343 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
?Annotation_U21_Trimmed_contig_7 = 60417 0 (0.000)coding (3/753 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
* ? Annotation_U21_Trimmed_contig_2 = 3759700 (0.000)228 (0.500) 58/256 2.6 100% coding (5343/5343 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
?Annotation_U21_Trimmed_contig_7 = 60419 0 (0.000)coding (1/753 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
* ? Annotation_U21_Trimmed_contig_9 1 =0 (0.000)1412 (0.850) 135/256 0.7 100% coding (1/936 nt) rasttk_feature_annotation_tool=annotate_proteins_km er_v2 Plasmid replication initiation protein
?Annotation_U21_Trimmed_contig_9 = 10661 NA (NA)intergenic (+719/–) rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– ORF9/–