TB-Profiler result

Run: SRR22528586
Summary

Run ID: SRR22528586

Sample name:

Date: 04-04-2023 04:19:20

Number of reads: 1061689

Percentage reads mapped: 99.75

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407713 c.489delA frameshift_variant 0.14 streptomycin
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 6196 c.957C>G synonymous_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8773 p.Gly491Val missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576163 c.816A>G synonymous_variant 0.11
mshA 576378 p.Asp344Gly missense_variant 0.15
mshA 576685 c.1338C>T synonymous_variant 0.18
ccsA 620444 p.Val185Glu missense_variant 0.2
rpoB 761446 p.Arg547Pro missense_variant 0.14
rpoB 762592 p.His929Leu missense_variant 0.2
rpoC 762686 c.-684G>C upstream_gene_variant 0.22
rpoB 763135 p.Gly1110Asp missense_variant 0.15
rpoB 763177 p.Ser1124* stop_gained 0.17
rpoC 764454 p.Ala362Val missense_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765223 c.1854G>A synonymous_variant 0.13
rpoC 765942 p.Lys858Arg missense_variant 0.17
rpoC 765981 p.Gly871Val missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775754 c.2727C>T synonymous_variant 0.14
mmpL5 775797 p.Phe895Ser missense_variant 0.15
mmpR5 779150 p.Glu54Val missense_variant 0.13
mmpR5 779303 p.Arg105Leu missense_variant 0.17
mmpS5 779581 c.-676G>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800992 p.Val62Ile missense_variant 0.15
fbiC 1302986 p.Pro19Leu missense_variant 0.13
fbiC 1303701 c.771C>T synonymous_variant 1.0
fbiC 1303990 c.1064delG frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472141 n.296G>A non_coding_transcript_exon_variant 0.14
rrs 1472743 n.898T>A non_coding_transcript_exon_variant 0.25
rrl 1474728 n.1071T>A non_coding_transcript_exon_variant 0.15
rrl 1476012 n.2355T>G non_coding_transcript_exon_variant 0.13
rpsA 1833511 c.-31G>A upstream_gene_variant 0.14
rpsA 1833529 c.-13G>T upstream_gene_variant 0.14
rpsA 1834109 p.Trp190Gly missense_variant 0.12
rpsA 1834957 c.1416C>G synonymous_variant 0.2
rpsA 1834976 p.Gly479Arg missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154504 c.1608C>A synonymous_variant 0.14
PPE35 2168585 c.2028T>A synonymous_variant 0.2
PPE35 2168734 p.Thr627Ala missense_variant 0.14
PPE35 2168995 p.Pro540Ser missense_variant 0.14
PPE35 2169123 p.Thr497Asn missense_variant 0.14
PPE35 2169131 c.1482C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289606 c.-365G>T upstream_gene_variant 0.15
pncA 2290189 c.-948G>T upstream_gene_variant 0.2
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715483 c.-151C>T upstream_gene_variant 0.15
ahpC 2726646 p.Gly152Ser missense_variant 0.15
ahpC 2726729 c.537C>G synonymous_variant 0.13
folC 2747584 p.Asn5Lys missense_variant 0.13
pepQ 2859676 p.Glu248Val missense_variant 0.13
pepQ 2860174 p.Tyr82Cys missense_variant 0.11
pepQ 2860248 c.171C>T synonymous_variant 0.15
ribD 2986922 c.84C>T synonymous_variant 0.13
ribD 2987350 p.Gly171Asp missense_variant 0.13
Rv2752c 3067128 c.-937A>G upstream_gene_variant 0.12
Rv2752c 3067178 c.-987G>A upstream_gene_variant 0.14
thyX 3067360 p.Ile196Phe missense_variant 0.14
thyX 3067631 p.Ser105Thr missense_variant 0.14
thyX 3067778 c.168C>T synonymous_variant 0.15
thyX 3067801 p.Lys49* stop_gained 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448597 p.Ile32Val missense_variant 0.15
Rv3083 3449017 p.Asp172His missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641036 p.Lys165Met missense_variant 0.13
fbiB 3642114 p.Val194Ile missense_variant 0.14
fbiB 3642167 c.633G>A synonymous_variant 0.14
fbiB 3642774 p.Leu414Val missense_variant 0.15
fbiB 3642823 p.Asp430Val missense_variant 0.15
rpoA 3878417 p.Gly31Ser missense_variant 0.95
ddn 3986745 c.-99A>G upstream_gene_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044212 p.Gly24Cys missense_variant 0.18
embC 4242182 p.Ala774Ser missense_variant 1.0
embC 4242437 p.Gln859Glu missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245625 p.Ser798Trp missense_variant 0.13
embA 4246261 p.Asp1010Val missense_variant 0.13
embB 4246754 p.Ala81Thr missense_variant 0.14
embB 4247055 p.Leu181Gln missense_variant 0.15
embB 4247916 p.Arg468Pro missense_variant 0.12
embB 4248209 p.Val566Met missense_variant 0.2
embB 4248619 c.2106G>C synonymous_variant 0.14
ubiA 4268971 c.862delG frameshift_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 0.93
whiB6 4338600 c.-79T>C upstream_gene_variant 0.88
gid 4407854 p.Gly117Arg missense_variant 0.92
gid 4408156 p.Leu16Arg missense_variant 1.0