TB-Profiler result

Run: SRR6046092
Summary

Run ID: SRR6046092

Sample name:

Date: 04-04-2023 12:11:01

Number of reads: 1496768

Percentage reads mapped: 98.94

Strain: lineage4.8

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.12 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5165 c.-75C>G upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.17
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.11
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.11
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.12
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.12
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.11
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.1
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474711 n.1054G>A non_coding_transcript_exon_variant 0.14
rrl 1474713 n.1056T>G non_coding_transcript_exon_variant 0.13
rrl 1474716 n.1059A>T non_coding_transcript_exon_variant 0.13
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.13
rrl 1474721 n.1064G>A non_coding_transcript_exon_variant 0.14
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.13
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.12
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.12
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.11
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.11
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.1
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.1
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.11
rrl 1475386 n.1729G>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448503 c.1_*1408del transcript_ablation 1.0