BRESEQ :: Marginal Predictions

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
*	Annotation_U21_Trimmed_contig_2	375,616	0	C	T	54.0%	619.1 / inf	970	N1663N (AAC→AAT)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	374,545	0	T	C	49.7%	18.9 / inf	940	H1306H (CAT→CAC)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	375,679	0	T	A	48.4%	1071.6 / inf	910	S1684S (TCT→TCA)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	374,503	0	C	T	45.2%	319.9 / inf	794	T1292T (ACC→ACT)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	375,682	0	C	A	44.8%	1286.0 / inf	831	V1685V (GTC→GTA)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	374,506	0	C	A	44.8%	513.8 / inf	802	S1293S (TCC→TCA)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	374,507	0	A	G	44.7%	401.9 / inf	803	I1294V (ATA→GTA)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	375,685	0	A	T	43.5%	1218.4 / inf	846	S1686S (TCA→TCT)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_10	2,247	0	T	C	41.5%	1252.3 / inf	1692	noncoding (891/2926 nt)	rasttk_feature_creation_tool=RNA_reps_LSU_rRNA	LSU rRNA ## 23S rRNA, large subunit ribosomal RNA
*	Annotation_U21_Trimmed_contig_2	375,697	0	G	A	40.9%	1138.3 / inf	693	S1690S (TCG→TCA)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_12	884	0	A	C	40.2%	262.0 / inf	481	noncoding (34/73 nt)	rasttk_feature_creation_tool=tRNAscan‑SE	tRNA‑Lys‑TTT
*	Annotation_U21_Trimmed_contig_2	375,704	0	A	G	38.2%	1234.5 / inf	650	T1693A (ACA→GCA) ‡	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	375,706	0	A	G	37.9%	1222.1 / inf	650	T1693T (ACA→ACG) ‡	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	375,573	0	T	C	36.0%	1069.2 / inf	644	I1649T (ATA→ACA)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_5	70,337	0	G	T	35.5%	632.0 / 105.0	359	H108N (CAT→AAT)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	hypothetical protein
*	Annotation_U21_Trimmed_contig_2	250,827	0	G	T	35.3%	607.5 / 127.7	386	intergenic (‑169/‑512)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2/rasttk_feature_annotation_tool=annotate_proteins_km er_v2	hypothetical protein/Uncharacterized MFS‑type transporter
*	Annotation_U21_Trimmed_contig_2	374,495	0	A	G	34.8%	1006.5 / inf	762	T1290A (ACT→GCT)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_2	374,491	0	C	T	34.3%	950.1 / inf	756	R1288R (CGC→CGT)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	Annotation_U21_Trimmed_contig_1	116,593	0	C	A	33.9%	383.1 / 99.3	227	intergenic (+127/‑341)	rasttk_feature_annotation_tool=annotate_proteins_si milarity/rasttk_feature_annotation_tool=annotate_proteins_km er_v2	RopB; Rgg‑like transcription regulator/hypothetical protein
*	Annotation_U21_Trimmed_contig_2	374,488	0	T	C	33.6%	1079.2 / inf	770	S1287S (AGT→AGC)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	Annotation_U21_Trimmed_contig_1	= 491259	0 (0.000)	126 (0.470)	45/254	3.2	52.1%	intergenic (‑304/–)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2/–	Pyruvate oxidase (EC 1.2.3.3)/–
*	?	Annotation_U21_Trimmed_contig_8	48167 =	232 (0.870)	126 (0.470)	45/254	3.2	52.1%	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_1	= 50	87 (0.320)	31 (0.370) +88 bp	8/80	4.0	50.7%	coding (50/567 nt)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	hypothetical protein
*	?	Annotation_U21_Trimmed_contig_1	55 =	106 (0.390)	31 (0.370) +88 bp	8/80	4.0	50.7%	coding (55/567 nt)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	hypothetical protein
*	?	Annotation_U21_Trimmed_contig_12	859 =	271 (1.000)	136 (0.580) +TCCGCCTGCCGGAGTT	33/224	4.5	53.4%	noncoding (59/73 nt)	rasttk_feature_creation_tool=tRNAscan‑SE	tRNA‑Lys‑TTT
*	?	Annotation_U21_Trimmed_contig_8	= 48531	0 (0.000)	136 (0.580) +TCCGCCTGCCGGAGTT	33/224	4.5	53.4%	intergenic (‑10/–)	rasttk_feature_creation_tool=tRNAscan‑SE/–	tRNA‑Ser‑GGA/–
*	?	Annotation_U21_Trimmed_contig_12	859 =	271 (1.000)	168 (0.660) +TCCGCCTGCCGGAGTT	33/224	4.5	58.6%	noncoding (59/73 nt)	rasttk_feature_creation_tool=tRNAscan‑SE	tRNA‑Lys‑TTT
*	?	Annotation_U21_Trimmed_contig_4	= 286779	0 (0.000)	168 (0.660) +TCCGCCTGCCGGAGTT	33/224	4.5	58.6%	intergenic (‑46/–)	rasttk_feature_creation_tool=tRNAscan‑SE/–	tRNA‑Thr‑CGT/–
*	?	Annotation_U21_Trimmed_contig_1	325750 =	266 (0.990)	83 (0.340) +GCCTGCCGGAGTT	23/230	7.5	41.0%	noncoding (63/74 nt)	rasttk_feature_creation_tool=tRNAscan‑SE	tRNA‑Asn‑GTT
*	?	Annotation_U21_Trimmed_contig_8	= 48531	0 (0.000)	83 (0.340) +GCCTGCCGGAGTT	23/230	7.5	41.0%	intergenic (‑10/–)	rasttk_feature_creation_tool=tRNAscan‑SE/–	tRNA‑Ser‑GGA/–
*	?	Annotation_U21_Trimmed_contig_2	= 375468	527 (1.210)	94 (0.210)	23/252	8.9	26.6%	coding (4841/5343 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)	94 (0.210)	23/252	8.9	26.6%	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_1	325750 =	266 (0.990)	76 (0.290) +GCCTGCCGGAGTT	18/230	9.4	38.9%	noncoding (63/74 nt)	rasttk_feature_creation_tool=tRNAscan‑SE	tRNA‑Asn‑GTT
*	?	Annotation_U21_Trimmed_contig_4	= 286779	0 (0.000)	76 (0.290) +GCCTGCCGGAGTT	18/230	9.4	38.9%	intergenic (‑46/–)	rasttk_feature_creation_tool=tRNAscan‑SE/–	tRNA‑Thr‑CGT/–
*	?	Annotation_U21_Trimmed_contig_2	= 375870	395 (0.900)	24 (0.060)	7/216	14.3	12.6%	coding (5243/5343 nt)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	?	Annotation_U21_Trimmed_contig_7	= 60399	0 (0.000)	24 (0.060)	7/216	14.3	12.6%	coding (21/753 nt)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)
*	?	Annotation_U21_Trimmed_contig_2	= 375183	410 (0.940)	26 (0.060)	8/252	15.3	11.4%	coding (4556/5343 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)	26 (0.060)	8/252	15.3	11.4%	coding (3/753 nt)	rasttk_feature_annotation_tool=annotate_proteins_km er_v2	Predicted cell‑wall‑anchored protein SasA (LPXTG motif)