TB-Profiler result

Run: SRR14088361
Summary

Run ID: SRR14088361

Sample name:

Date: 03-04-2023 09:45:36

Number of reads: 807300

Percentage reads mapped: 99.54

Strain: lineage3.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 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 761110 p.Asp435Gly missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 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 6658 c.-644G>A upstream_gene_variant 0.11
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 491742 c.960T>C synonymous_variant 1.0
mshA 576751 p.Lys468Asn missense_variant 0.25
ccsA 620092 c.202C>A synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761277 p.Ile491Leu missense_variant 1.0
rpoB 762259 p.Ile818Thr missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766917 p.Arg1183Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>G synonymous_variant 0.12
mmpL5 776003 c.2478C>T synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776192 c.2289G>T synonymous_variant 0.11
mmpR5 779109 p.Leu40Phe missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303251 c.321C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834950 p.Leu470Pro missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.1
PPE35 2169902 p.Leu237Phe missense_variant 0.14
Rv1979c 2223047 p.Ile40Phe missense_variant 0.12
Rv1979c 2223113 p.Ser18Gly missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726116 c.-77T>G upstream_gene_variant 1.0
folC 2747645 c.-47G>A upstream_gene_variant 0.11
Rv2752c 3064529 p.Val555Ile missense_variant 0.12
thyX 3067351 p.Arg199Trp missense_variant 0.14
thyA 3074648 c.-177T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612700 p.Asp139Glu missense_variant 0.18
rpoA 3877850 p.Gly220Ser missense_variant 0.11
clpC1 4040057 c.648C>T synonymous_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.13
embC 4241651 p.Ala597Thr missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242308 p.Thr816Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249535 p.Glu1008* stop_gained 0.13
aftB 4267716 p.Ala374Glu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407703 p.Ala167Asp missense_variant 1.0