TB-Profiler result

Run: SRR6855729
Summary

Run ID: SRR6855729

Sample name:

Date: 04-04-2023 17:43:43

Number of reads: 580183

Percentage reads mapped: 99.08

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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 2154765 c.1346delT frameshift_variant 0.14 isoniazid
ethA 4326273 c.1200delG frameshift_variant 0.15 ethionamide
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
fgd1 490712 c.-71T>A upstream_gene_variant 0.11
ccsA 620579 p.Tyr230Cys missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765994 c.2625A>G synonymous_variant 0.11
rpoC 766006 c.2640_2641delGT frameshift_variant 0.12
rpoC 766070 c.2701C>T synonymous_variant 1.0
rpoC 766450 c.3081T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776545 p.Lys646Glu missense_variant 0.13
mmpL5 777347 c.1134C>A synonymous_variant 0.29
mmpL5 778305 p.Ile59Thr missense_variant 1.0
mmpR5 779254 p.Arg89Trp missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.14
rrl 1475036 n.1379G>T non_coding_transcript_exon_variant 0.14
fabG1 1673872 p.Trp145Arg missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102979 p.Ser22Pro missense_variant 0.1
katG 2155677 c.435C>A synonymous_variant 0.11
PPE35 2167969 p.Pro882Ser missense_variant 0.15
PPE35 2168771 c.1842A>G synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714982 c.351A>G synonymous_variant 0.12
eis 2715028 p.Ala102Asp missense_variant 0.17
pepQ 2859833 p.Ala196Ser missense_variant 0.18
ald 3086725 c.-95A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087617 c.798T>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568565 p.Ala39Ser missense_variant 0.2
fbiA 3641447 p.Thr302Met missense_variant 0.95
alr 3840812 c.609T>C synonymous_variant 0.1
rpoA 3877553 p.Glu319Lys missense_variant 0.96
clpC1 4038616 p.Val697Phe missense_variant 0.13
clpC1 4038644 p.Glu687Asp missense_variant 0.11
clpC1 4040492 c.213G>A synonymous_variant 0.12
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241208 p.Leu449Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248616 c.2103G>T synonymous_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268552 c.284delT frameshift_variant 0.14
ethA 4327400 p.Asp25Gly missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0