TB-Profiler result

Run: SRR1173725
Summary

Run ID: SRR1173725

Sample name:

Date: 03-04-2023 03:30:33

Number of reads: 1926526

Percentage reads mapped: 93.57

Strain: lineage8

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
lineage8 Lineage 8 None 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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpoB 761127 p.Ser441Ala missense_variant 0.5 rifampicin
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288988 p.Leu85Arg missense_variant 0.19 pyrazinamide
pncA 2289081 p.Pro54Gln missense_variant 0.78 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.71 ethambutol
embB 4247495 p.Asp328Tyr missense_variant 0.46 ethambutol
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 8553 p.Arg418Trp missense_variant 1.0
gyrA 9088 p.Val596Ala missense_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775611 p.Ser957* stop_gained 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779192 p.Ser68Ile missense_variant 0.46
mmpS5 779536 c.-631G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406466 p.Ser292Leu missense_variant 1.0
embR 1417464 c.-117C>T upstream_gene_variant 1.0
atpE 1461057 p.Ile5Leu missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.92
rrs 1472905 n.1060C>T non_coding_transcript_exon_variant 0.17
rrl 1475841 n.2184T>G non_coding_transcript_exon_variant 0.22
fabG1 1673219 c.-221C>T upstream_gene_variant 0.12
tlyA 1917786 c.-154G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155155 c.957C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168701 p.Val638Ile missense_variant 1.0
PPE35 2168924 c.1689G>T synonymous_variant 0.99
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.92
eis 2714418 c.915C>T synonymous_variant 1.0
ahpC 2726247 p.Ile19Val missense_variant 0.29
pepQ 2859482 p.Ala313Thr missense_variant 1.0
thyA 3074400 c.72C>G synonymous_variant 1.0
thyA 3074591 c.-120T>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449865 c.1362G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612035 p.Val361Gly missense_variant 0.15
Rv3236c 3612540 p.Leu193Phe missense_variant 1.0
alr 3840800 c.621C>A synonymous_variant 1.0
rpoA 3878403 c.105C>A synonymous_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>A upstream_gene_variant 0.29
embA 4245411 p.Ser727Cys missense_variant 0.2
embB 4247252 p.Ser247Ala missense_variant 1.0
embB 4247483 p.Gly324Arg missense_variant 0.58
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248022 p.Leu503Phe missense_variant 1.0
embB 4248206 p.Ser565Gly missense_variant 1.0
aftB 4267683 p.Trp385Ser missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326264 p.Arg404Cys missense_variant 1.0
ethA 4327442 p.Gly11Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407760 c.442_443insC frameshift_variant 1.0