TB-Profiler result

Run: SRR1173201
Summary

Run ID: SRR1173201

Sample name:

Date: 03-04-2023 03:18:58

Number of reads: 821253

Percentage reads mapped: 97.53

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761155 p.Ser450Trp missense_variant 0.94 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491207 p.Leu142Pro missense_variant 0.11
mshA 575998 c.651C>T synonymous_variant 0.25
ccsA 620830 p.Thr314Ser missense_variant 0.11
rpoB 761032 p.Gln409Arg missense_variant 0.95
rpoB 761467 p.Leu554Pro missense_variant 1.0
rpoB 763216 p.Ala1137Val missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778921 c.-441G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304869 c.1939C>T synonymous_variant 0.11
fbiC 1304875 p.Ile649Val missense_variant 0.11
fbiC 1304893 p.Gly655Ser missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 0.97
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156011 p.Gly34Glu missense_variant 0.1
PPE35 2169320 p.Leu431Phe missense_variant 0.38
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714355 c.978C>T synonymous_variant 0.18
Rv2752c 3065824 p.Pro123Leu 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 3612488 c.628delG frameshift_variant 0.12
alr 3840359 c.1062G>T synonymous_variant 0.12
rpoA 3878555 c.-48G>T upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038755 c.1950G>A synonymous_variant 0.13
embC 4239863 c.1A>G start_lost 1.0
embC 4241089 c.1227C>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269549 c.-713C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
pncA 2288947 c.-606_294del start_lost&conservative_inframe_deletion 1.0
gid 4407912 c.160_290del frameshift_variant 1.0