TB-Profiler result

Run: SRR7131104
Summary

Run ID: SRR7131104

Sample name:

Date: 04-04-2023 18:45:14

Number of reads: 1547523

Percentage reads mapped: 99.99

Strain: lineage4.3.4.2

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 1472644 n.799C>T 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778996 p.Val3Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.1
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.1
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.14
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.19
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.17
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.17
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.18
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.19
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.18
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.18
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.2
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.18
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.18
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.17
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.17
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.17
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.21
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.13
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.24
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.19
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.19
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.2
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.14
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.15
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.15
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.14
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.34
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.34
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519221 c.1107G>A synonymous_variant 1.0
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0