TB-Profiler result

Run: SRR6982538
Summary

Run ID: SRR6982538

Sample name:

Date: 04-04-2023 18:40:26

Number of reads: 296771

Percentage reads mapped: 99.71

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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
mshA 576785 p.Ala480Ser missense_variant 0.18
rpoC 764137 p.Met256Ile missense_variant 0.11
rpoC 766863 p.Val1165Glu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 c.1362C>T synonymous_variant 0.2
mmpL5 777239 c.1242C>T synonymous_variant 0.14
mmpL5 778137 p.Arg115Lys missense_variant 1.0
mmpL5 778852 c.-372C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801113 p.Thr102Ile missense_variant 0.18
fbiC 1303074 p.Met48Ile missense_variant 0.11
fbiC 1303980 c.1050G>T synonymous_variant 0.15
Rv1258c 1406941 c.400C>A synonymous_variant 0.15
Rv1258c 1407433 c.-93A>G upstream_gene_variant 0.13
embR 1416999 p.Ala117Thr missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473837 n.180G>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474555 n.898T>G non_coding_transcript_exon_variant 0.11
rrl 1474926 n.1269C>G non_coding_transcript_exon_variant 0.11
rrl 1476018 n.2361G>T non_coding_transcript_exon_variant 0.11
fabG1 1673162 c.-278T>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102791 c.252A>G synonymous_variant 0.15
katG 2154439 p.Ala558Gly missense_variant 0.2
katG 2155096 p.Tyr339Phe missense_variant 0.14
PPE35 2167671 p.Phe981Ser missense_variant 0.14
PPE35 2168460 p.Asn718Ile missense_variant 0.14
PPE35 2169736 p.Gly293Arg missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715381 c.-49C>T upstream_gene_variant 0.11
eis 2715397 c.-65T>G upstream_gene_variant 0.12
Rv2752c 3065357 p.Leu279Ile missense_variant 0.11
Rv2752c 3065433 c.759G>A synonymous_variant 0.12
fprA 3474480 c.474C>T synonymous_variant 0.14
Rv3236c 3612047 p.Ala357Val missense_variant 1.0
Rv3236c 3613265 c.-149C>T upstream_gene_variant 0.11
alr 3840205 p.Glu406Lys missense_variant 0.11
alr 3840226 p.Thr399Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243435 p.Arg68His missense_variant 0.17
aftB 4266977 c.1860G>A synonymous_variant 1.0
aftB 4268424 p.Gly138Val missense_variant 1.0
ubiA 4269613 p.Asp74Gly missense_variant 0.18
whiB6 4338199 p.Asp108Val missense_variant 0.11
whiB6 4338479 p.Phe15Leu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407932 c.269_270delTC frameshift_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
ethR 4326192 c.-1356_265del frameshift_variant 1.0