TB-Profiler result

Run: SRR6896374
Summary

Run ID: SRR6896374

Sample name:

Date: 04-04-2023 18:04:01

Number of reads: 313455

Percentage reads mapped: 99.63

Strain: lineage4.3.2.1

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
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.99
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
katG 2154246 c.1865delC frameshift_variant 0.11 isoniazid, isoniazid
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491768 p.Ala329Val missense_variant 0.12
rpoB 760464 p.Ile220Val missense_variant 0.17
rpoB 760927 p.Thr374Met missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765542 p.Thr725Ala missense_variant 0.1
rpoC 766892 p.Phe1175Ile missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776499 p.Gly661Ala missense_variant 0.14
mmpL5 779286 c.-806A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781845 p.Lys96* stop_gained 0.11
fbiC 1304327 p.Leu466Gln missense_variant 0.15
fbiC 1304592 p.Phe554Leu missense_variant 0.12
fbiC 1305329 p.Leu800His missense_variant 0.13
fbiC 1305332 p.Glu801Gly missense_variant 0.13
Rv1258c 1406190 p.Ala384Val missense_variant 0.12
Rv1258c 1406883 p.Ala153Val missense_variant 0.13
Rv1258c 1406926 c.415T>C synonymous_variant 0.13
embR 1417033 p.Ile105Met missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473775 n.118A>G non_coding_transcript_exon_variant 0.14
fabG1 1673820 p.Met127Ile missense_variant 0.13
inhA 1674926 p.Val242Ala missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102175 c.867delT frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289044 c.198G>A synonymous_variant 0.11
pncA 2289441 c.-200C>T upstream_gene_variant 0.13
eis 2714252 p.Leu361Phe missense_variant 0.11
eis 2714968 p.Glu122Gly missense_variant 0.2
ahpC 2726377 c.186delT frameshift_variant 0.11
pepQ 2860471 c.-53C>T upstream_gene_variant 0.22
ribD 2987133 p.Gly99Cys missense_variant 0.14
ribD 2987404 p.Arg189Gln missense_variant 0.11
ribD 2987532 p.Gly232Arg missense_variant 0.22
Rv2752c 3064679 p.Glu505Lys missense_variant 0.11
Rv2752c 3067136 c.-945A>T upstream_gene_variant 0.13
thyX 3067886 c.59delC frameshift_variant 0.14
thyA 3073752 c.720G>A synonymous_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448912 p.Ile137Val missense_variant 0.11
Rv3083 3448928 p.Tyr142Cys missense_variant 0.1
Rv3083 3449349 c.846C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568541 p.Pro47Ser missense_variant 0.18
Rv3236c 3612384 p.Phe245Leu missense_variant 0.17
fbiA 3640433 c.-110T>C upstream_gene_variant 0.12
fbiA 3641186 p.Asn215Ser missense_variant 0.17
fbiB 3642370 p.Ala279Val missense_variant 0.13
ddn 3986883 p.Ser14Gly missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040521 p.Gln62Lys missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244974 p.Ala581Val missense_variant 0.22
embB 4248674 p.Ser721Pro missense_variant 0.22
embB 4248791 p.Asn760Asp missense_variant 0.11
aftB 4267748 c.1089T>C synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407582 c.621T>C synonymous_variant 1.0
gid 4408125 p.Leu26Phe missense_variant 0.1
gid 4408156 p.Leu16Arg missense_variant 0.95