TB-Profiler result

Run: SRR6896553
Summary

Run ID: SRR6896553

Sample name:

Date: 04-04-2023 18:09:41

Number of reads: 314672

Percentage reads mapped: 99.69

Strain: lineage4.3.4.2.1

Drug-resistance: Other

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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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
gid 4407876 c.326delG frameshift_variant 0.11 streptomycin
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 6140 p.Val301Leu missense_variant 1.0
gyrB 6326 p.Ser363Arg missense_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
gyrA 9410 p.Met703Ile missense_variant 0.15
mshA 576004 p.Asp219Glu missense_variant 0.14
ccsA 620100 c.210G>A synonymous_variant 0.15
ccsA 620245 p.Leu119Met missense_variant 0.13
rpoB 760935 p.Glu377* stop_gained 0.15
rpoB 761258 p.Glu484Asp missense_variant 0.15
rpoB 762630 p.Ala942Ser missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765482 p.Pro705Thr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 0.94
mmpL5 776027 c.2454G>A synonymous_variant 0.15
mmpS5 778500 p.Tyr136His missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303964 p.Ala345Glu missense_variant 0.11
fbiC 1305339 c.2409C>G synonymous_variant 0.13
Rv1258c 1406545 p.Ala266Ser missense_variant 0.14
embR 1416942 p.Arg136Ser missense_variant 0.18
atpE 1460905 c.-140T>A upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674111 c.-91G>T upstream_gene_variant 0.17
rpsA 1833629 p.Ile30Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154020 p.Phe698Ile missense_variant 0.2
katG 2155630 p.Trp161Leu missense_variant 0.11
katG 2155797 p.Met105Ile missense_variant 0.12
PPE35 2167745 c.2868C>A synonymous_variant 0.12
PPE35 2168445 p.Pro723Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859585 c.834C>A synonymous_variant 0.22
pepQ 2860226 p.Ala65Ser missense_variant 0.17
ribD 2987166 p.Gly110Cys missense_variant 0.12
thyX 3067248 p.Thr233Ile missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338979 c.-139G>T upstream_gene_variant 0.14
Rv3083 3448391 c.-113C>A upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474492 c.486G>C synonymous_variant 1.0
fprA 3474986 p.Val327Ala missense_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612247 p.Met290Ile missense_variant 0.13
Rv3236c 3613018 p.Ile33Met missense_variant 0.25
fbiA 3640470 c.-73T>C upstream_gene_variant 0.14
fbiA 3640660 p.Gln40Lys missense_variant 0.18
fbiA 3641060 p.Trp173Leu missense_variant 0.12
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877707 c.801G>A synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.92
clpC1 4038350 c.2355C>A synonymous_variant 0.12
clpC1 4040016 p.Ala230Val missense_variant 0.15
clpC1 4040320 p.Ala129Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244980 p.Val583Ala missense_variant 0.17
embA 4245493 p.Pro754Leu missense_variant 0.15
embA 4245825 p.Asp865Tyr missense_variant 0.18
embB 4249299 p.Trp929* stop_gained 0.13
aftB 4267462 p.Gln459Glu missense_variant 0.14
ethR 4327587 p.Arg13Ser missense_variant 0.12
ethR 4327987 p.Ala147Ser missense_variant 0.12
whiB6 4338552 c.-31A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0