TB-Profiler result

Run: SRR4035626

Summary

Run ID: SRR4035626

Sample name:

Date: 04-04-2023 07:13:23

Number of reads: 968683

Percentage reads mapped: 99.75

Strain: lineage4.3.4.2.1

Drug-resistance: Sensitive


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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
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 5674 c.436delT frameshift_variant 0.18
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 6940 c.-362G>A upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620326 c.436C>T synonymous_variant 0.11
ccsA 620688 c.798G>T synonymous_variant 0.13
rpoB 761986 c.2183_2184delCG frameshift_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779255 p.Arg89Gln missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801186 c.378C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472401 n.559delG non_coding_transcript_exon_variant 0.18
rrs 1472433 n.588G>T non_coding_transcript_exon_variant 0.17
rpsA 1833747 p.Ser69Cys missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289460 c.-219G>T upstream_gene_variant 0.12
kasA 2518222 c.108G>A synonymous_variant 0.12
kasA 2518308 p.Lys65Arg missense_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.25
pepQ 2860295 p.Ala42Thr missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339308 p.Pro64His missense_variant 0.11
Rv3083 3448730 p.Ala76Val missense_variant 0.17
Rv3083 3449436 c.933G>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612169 c.947delA frameshift_variant 0.13
Rv3236c 3612578 p.Glu180Gly missense_variant 0.12
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840732 p.Glu230Val missense_variant 0.11
rpoA 3878169 c.339G>A synonymous_variant 0.15
ddn 3986849 c.6G>A synonymous_variant 0.12
ddn 3986858 c.15G>A synonymous_variant 0.12
ddn 3987048 p.Asp69Asn missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240704 c.844delG frameshift_variant 0.14
embC 4241436 p.Ala525Asp missense_variant 0.27
embC 4242425 p.Arg855Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245205 p.Gly658Glu missense_variant 0.1
embB 4248867 p.Pro785Gln missense_variant 0.12
aftB 4267475 c.1362G>T synonymous_variant 0.12
ethA 4328157 c.-684C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0