TB-Profiler result

Run: SRR1169313
Summary

Run ID: SRR1169313

Sample name:

Date: 03-04-2023 02:51:16

Number of reads: 691586

Percentage reads mapped: 97.59

Strain: lineage4.1.1

Drug-resistance: MDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Cys missense_variant 1.0 pyrazinamide
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 9304 p.Gly668Asp missense_variant 1.0
ccsA 619812 c.-79C>A upstream_gene_variant 0.33
rpoC 763669 c.300C>A synonymous_variant 0.13
rpoC 764923 c.1554A>G synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765359 p.Ala664Ser missense_variant 0.17
rpoC 765608 p.Asp747Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776094 p.Arg796Pro missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304484 c.1554C>A synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473263 n.1418A>T non_coding_transcript_exon_variant 0.17
rrl 1475324 n.1667G>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103150 c.-108T>C upstream_gene_variant 0.11
Rv1979c 2222401 p.Ala255Val missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288723 p.Glu173Asp missense_variant 0.2
pncA 2289160 p.Ala28Thr missense_variant 0.17
eis 2714933 p.Ala134Ser missense_variant 0.13
ahpC 2726210 c.18T>C synonymous_variant 1.0
ribD 2986865 c.27C>A synonymous_variant 0.15
Rv2752c 3067099 c.-908C>A upstream_gene_variant 0.18
Rv2752c 3067179 c.-988T>C upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243267 p.Ile12Thr missense_variant 0.11
embA 4246318 p.Pro1029Gln missense_variant 0.11
embB 4247495 p.Asp328His missense_variant 1.0
embB 4248073 c.1560C>G synonymous_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407935 p.Leu90Phe missense_variant 0.94
gid 4408142 c.61C>A synonymous_variant 0.14