TB-Profiler result

Run: SRR2101626
Summary

Run ID: SRR2101626

Sample name:

Date: 03-04-2023 23:49:34

Number of reads: 441615

Percentage reads mapped: 99.64

Strain: lineage4.3.4.2.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
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
katG 2155843 p.Trp90* stop_gained 0.12 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 6140 p.Val301Leu missense_variant 1.0
gyrB 6222 p.Val328Gly missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7670 c.369A>G synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764186 p.Glu273Lys missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767152 c.3783T>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406433 p.Met303Thr missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472134 n.289C>T non_coding_transcript_exon_variant 0.13
rrl 1475091 n.1434G>C non_coding_transcript_exon_variant 0.12
fabG1 1673852 p.Ile138Lys missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102298 p.Val249Phe missense_variant 0.12
katG 2155848 p.Gln88His missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.96
folC 2747343 c.253_255delCTG conservative_inframe_deletion 0.12
pepQ 2860158 c.261C>T synonymous_variant 0.13
pepQ 2860263 c.156C>T synonymous_variant 0.13
ribD 2986770 c.-69A>T upstream_gene_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074476 c.-5C>A upstream_gene_variant 0.13
thyA 3074599 c.-128T>C upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087888 p.Thr357Ser missense_variant 0.15
fbiD 3339410 p.Ala98Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247246 c.737delG frameshift_variant 0.13
aftB 4267495 p.Gly448Trp missense_variant 0.17
aftB 4268433 p.Ala135Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0