TB-Profiler result

Run: SRR6256995
Summary

Run ID: SRR6256995

Sample name:

Date: 04-04-2023 13:22:14

Number of reads: 692018

Percentage reads mapped: 99.55

Strain: lineage4.2.1.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4246734 p.Leu74Arg missense_variant 1.0 ethambutol
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 9243 p.Ile648Phe missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576164 p.Arg273Ser missense_variant 0.17
mshA 576387 p.Ala347Val missense_variant 0.11
rpoC 767155 c.3786C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303750 c.820T>C synonymous_variant 0.12
embR 1417211 p.Arg46Leu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473777 n.120T>A non_coding_transcript_exon_variant 0.11
inhA 1673502 c.-700C>A upstream_gene_variant 0.11
rpsA 1834517 p.Leu326Met missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168751 p.Ser621Ile missense_variant 0.12
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714659 p.Leu225Pro missense_variant 0.12
Rv2752c 3065445 c.747C>T synonymous_variant 0.12
thyA 3073703 p.Ile257Phe missense_variant 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841040 p.Asp127Glu missense_variant 0.11
rpoA 3878440 p.Ile23Thr missense_variant 0.14
clpC1 4038969 p.Gln579Arg missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243130 p.Pro1090Thr missense_variant 0.11
embA 4245681 p.Gly817Ser missense_variant 0.14
embB 4246516 c.3G>T start_lost 0.12
embB 4246534 p.Arg7Ser missense_variant 0.17
embB 4246622 p.Gly37Ser missense_variant 0.12
embB 4247010 c.500delC frameshift_variant 0.12
aftB 4267232 p.Asp535Glu missense_variant 0.14
aftB 4269708 c.-872C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0