TB-Profiler result

Run: SRR12830371
Summary

Run ID: SRR12830371

Sample name:

Date: 03-04-2023 06:58:29

Number of reads: 397594

Percentage reads mapped: 99.87

Strain: lineage4.3.4.2

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 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;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 2155897 p.Asp72Gly missense_variant 0.1 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 0.14 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 8434 p.Thr378Ser missense_variant 1.0
gyrA 8988 p.Thr563Pro missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576710 c.1363C>A synonymous_variant 0.15
rpoC 763472 p.Asn35Asp missense_variant 0.22
rpoC 763690 p.Phe107Leu missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776842 p.Ala547Ser missense_variant 0.13
mmpR5 778124 c.-866G>A upstream_gene_variant 0.12
mmpL5 778286 p.Ser65Arg missense_variant 0.14
mmpL5 778699 c.-219C>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303720 p.Gly264Cys missense_variant 0.12
fbiC 1303758 c.828G>T synonymous_variant 0.14
fbiC 1304445 c.1515G>A synonymous_variant 0.12
Rv1258c 1406690 c.651C>G synonymous_variant 0.1
atpE 1461219 c.175T>C synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471905 n.60G>A non_coding_transcript_exon_variant 0.17
rrs 1473215 n.1370A>G non_coding_transcript_exon_variant 0.23
rrl 1473778 n.121G>A non_coding_transcript_exon_variant 0.18
rrl 1474143 n.486T>C non_coding_transcript_exon_variant 0.18
inhA 1674643 p.Asp148Tyr missense_variant 0.12
rpsA 1833492 c.-50G>A upstream_gene_variant 0.14
rpsA 1834465 c.924T>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153922 p.Lys730Asn missense_variant 0.13
katG 2156409 c.-298G>T upstream_gene_variant 0.13
PPE35 2168976 p.Ala546Val missense_variant 0.12
PPE35 2170125 p.Val163Ala missense_variant 0.11
PPE35 2170478 c.135C>T synonymous_variant 0.12
PPE35 2170529 c.84G>T synonymous_variant 0.14
Rv1979c 2222869 p.Ala99Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518013 c.-102G>T upstream_gene_variant 0.11
ahpC 2726470 c.281delT frameshift_variant 0.4
ahpC 2726577 p.Gly129Ser missense_variant 0.18
ahpC 2726657 c.465A>G synonymous_variant 0.12
folC 2746460 p.Ser380Ile missense_variant 0.13
Rv2752c 3065280 c.912C>A synonymous_variant 0.14
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
Rv2752c 3066154 p.Ser13Tyr missense_variant 0.15
thyA 3073820 p.Leu218Met missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074128 p.Ala115Glu missense_variant 0.17
ald 3086706 c.-114T>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474159 c.153C>T synonymous_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640778 p.Trp79Leu missense_variant 0.15
alr 3841020 p.Ser134Leu missense_variant 0.13
rpoA 3878472 c.36C>T synonymous_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038834 p.Phe624Ser missense_variant 0.12
clpC1 4038901 p.Val602Ile missense_variant 0.15
clpC1 4040499 p.Gln69Arg missense_variant 0.17
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247884 c.1371C>A synonymous_variant 1.0
embB 4249205 p.Val898Leu missense_variant 0.12
ubiA 4269407 p.Lys143Glu missense_variant 0.12
ubiA 4269424 p.Ala137Glu missense_variant 0.14
ethA 4326441 p.Asn345Tyr missense_variant 0.14
ethR 4327745 p.Pro66Gln missense_variant 0.18
ethR 4327964 p.Ser139* stop_gained 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0