TB-Profiler result

Run: SRR6981963
Summary

Run ID: SRR6981963

Sample name:

Date: 04-04-2023 18:23:14

Number of reads: 728343

Percentage reads mapped: 98.72

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9474 p.Val725Leu missense_variant 0.1
mshA 575648 p.Val101Leu missense_variant 0.15
mshA 576488 p.Val381His missense_variant 0.14
ccsA 620267 c.379delG frameshift_variant 0.12
rpoB 760944 p.Gln380Glu missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778994 p.Ser2Asn missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407126 p.Arg72Leu missense_variant 0.2
embR 1416734 c.613delG frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 1472767 n.922G>A non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.18
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.16
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.15
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.15
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.16
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.16
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.16
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.16
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.16
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.15
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.16
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.16
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.16
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.22
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.17
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.11
fabG1 1674068 p.Arg210Leu missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102289 p.Val252Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290000 c.-759C>A upstream_gene_variant 0.12
folC 2747548 c.51C>T synonymous_variant 0.11
pepQ 2860277 c.141dupC frameshift_variant 0.11
ribD 2987468 c.630G>A synonymous_variant 0.18
thyX 3067353 p.Met198Thr missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339371 p.Pro85His missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3642281 c.747C>G synonymous_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241542 c.1680C>A synonymous_variant 0.13
embC 4241973 p.Val704Ala missense_variant 0.14
embC 4242115 c.2253G>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244905 p.Val558Asp missense_variant 0.29
embA 4245119 c.1887C>T synonymous_variant 0.14
embB 4246811 p.Gly100Cys missense_variant 0.11
embB 4246994 p.Phe161Leu missense_variant 0.12
embB 4248842 c.2329T>C synonymous_variant 0.12
aftB 4268504 c.333G>T synonymous_variant 0.11
aftB 4268557 p.Gly94Arg missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0