TB-Profiler result

Run: SRR4033985
Summary

Run ID: SRR4033985

Sample name:

Date: 04-04-2023 06:29:27

Number of reads: 777156

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

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
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 2153946 c.2165delA frameshift_variant 0.14 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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8847 p.Val516Ile missense_variant 0.17
gyrA 9253 p.Val651Ala missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575555 p.Val70Ile missense_variant 0.2
rpoB 759943 p.Gly46Val missense_variant 0.17
rpoB 761823 p.Asn673Asp missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765159 p.Gly597Asp missense_variant 0.15
rpoC 765470 p.Ala701Thr missense_variant 0.18
rpoC 765480 p.Tyr704Cys missense_variant 0.17
rpoC 765822 p.Ala818Val missense_variant 0.33
rpoC 767249 p.Ser1294Gly missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776199 p.Thr761Ile missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416787 c.561C>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>C upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474431 n.774G>T non_coding_transcript_exon_variant 0.13
rrl 1475609 n.1952C>A non_coding_transcript_exon_variant 0.11
rrl 1476326 n.2673dupA non_coding_transcript_exon_variant 0.14
inhA 1674895 p.Met232Val missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102711 p.Pro111His missense_variant 0.13
ndh 2102824 c.219G>A synonymous_variant 0.13
ndh 2103192 c.-150G>T upstream_gene_variant 0.12
katG 2154852 p.Met420Ile missense_variant 0.33
katG 2155975 p.Lys46Met missense_variant 0.18
katG 2156042 p.Gly24Cys missense_variant 0.11
Rv1979c 2222165 p.Gly334Trp missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289749 c.-508G>A upstream_gene_variant 0.33
kasA 2518288 c.174C>A synonymous_variant 0.29
ahpC 2726293 p.Tyr34Cys missense_variant 1.0
Rv2752c 3067039 c.-848T>G upstream_gene_variant 0.15
thyX 3067873 p.Trp25Arg missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086837 c.18G>A synonymous_variant 0.14
fbiD 3339176 p.Ala20Asp missense_variant 0.25
Rv3083 3449362 c.863dupC frameshift_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840348 p.Ala358Asp missense_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038832 p.Asp625Tyr missense_variant 0.18
clpC1 4040013 p.Gln231Arg missense_variant 0.11
clpC1 4040466 p.Phe80Tyr missense_variant 0.18
panD 4044230 p.Ala18Thr missense_variant 0.18
embC 4241551 c.1689A>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242841 c.-392C>T upstream_gene_variant 0.15
embA 4242964 c.-269C>A upstream_gene_variant 0.2
aftB 4268267 c.570G>T synonymous_variant 0.29
aftB 4268763 p.Arg25His missense_variant 0.17
aftB 4269447 c.-611C>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338677 c.-156G>T upstream_gene_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0