TB-Profiler result

Run: SRR16151359
Summary

Run ID: SRR16151359

Sample name:

Date: 03-04-2023 16:30:54

Number of reads: 457426

Percentage reads mapped: 99.68

Strain: lineage4.3.2

Drug-resistance: MDR-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 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
rpoB 761130 p.Gly442Trp missense_variant 0.11 rifampicin
katG 2155853 c.254_258delCCACC frameshift_variant 0.5 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
gyrB 6026 p.His263Asp missense_variant 0.17
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrB 7262 p.Val675Ile missense_variant 0.14
gyrA 7307 c.6A>T synonymous_variant 0.12
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 491521 c.739C>A synonymous_variant 0.13
mshA 575643 p.Pro99Gln missense_variant 0.11
mshA 576277 c.930C>T synonymous_variant 0.11
rpoB 760070 c.264T>A synonymous_variant 0.15
rpoB 760089 p.Gly95Trp missense_variant 0.18
rpoB 760214 c.408C>T synonymous_variant 0.17
rpoB 762212 c.2406G>T synonymous_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765213 p.Pro615Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 p.His825Gln missense_variant 0.12
mmpL5 776348 c.2133G>T synonymous_variant 0.13
mmpR5 778139 c.-851G>T upstream_gene_variant 0.11
mmpL5 778615 c.-135G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800880 c.72A>G synonymous_variant 0.13
rplC 801127 p.Ala107Ser missense_variant 0.12
rplC 801142 p.Val112Phe missense_variant 0.13
Rv1258c 1406333 c.1008A>T synonymous_variant 0.1
Rv1258c 1407112 p.Val77Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154716 p.Gly466* stop_gained 0.76
katG 2154790 p.Pro441Leu missense_variant 0.12
Rv1979c 2222907 c.258T>C synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288759 c.483G>T synonymous_variant 0.12
pncA 2289933 c.-692G>A upstream_gene_variant 0.15
pepQ 2859932 p.Leu163Met missense_variant 0.15
pepQ 2860468 c.-52_-51delGC upstream_gene_variant 0.11
ribD 2986832 c.-7C>A upstream_gene_variant 0.14
ribD 2986928 p.Gln30His missense_variant 0.2
Rv2752c 3066038 p.His52Tyr missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074493 c.-22C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087539 c.720G>A synonymous_variant 0.12
fprA 3473885 c.-122G>A upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612840 p.Ala93Thr missense_variant 0.12
fbiA 3641435 p.Ile298Thr missense_variant 0.12
alr 3840631 p.Pro264Thr missense_variant 0.11
alr 3841554 c.-134T>C upstream_gene_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244229 p.Ile333Phe missense_variant 0.14
embB 4246526 p.Ala5Thr missense_variant 0.15
embB 4247461 p.Met316Ile missense_variant 0.11
embB 4247613 p.Arg367His missense_variant 0.11
aftB 4268355 p.Pro161Gln missense_variant 0.15
aftB 4268532 p.Thr102Ile missense_variant 0.12
aftB 4268867 c.-31G>T upstream_gene_variant 0.11
whiB6 4338362 c.160C>A synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0