TB-Profiler result

Run: SRR3105742
Summary

Run ID: SRR3105742

Sample name:

Date: 04-04-2023 05:07:06

Number of reads: 1471274

Percentage reads mapped: 98.44

Strain: lineage3;lineage2.2.1

Drug-resistance: Pre-XDR-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 0.44
lineage2 East-Asian Beijing RD105 0.55
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.61
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.57
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
gyrB 6620 p.Asp461Asn missense_variant 0.38 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.32 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 0.65 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.34 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.3 pyrazinamide, pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.43 ethambutol
embB 4247429 p.Met306Val missense_variant 0.47 ethambutol
embB 4247723 p.Pro404Ser missense_variant 0.61 ethambutol
ethA 4326547 c.926dupA frameshift_variant 0.5 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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.55
ccsA 620625 p.Ile245Met missense_variant 0.47
rpoB 759746 c.-61C>T upstream_gene_variant 0.32
rpoB 760321 p.Gln172Arg missense_variant 0.4
rpoC 762434 c.-936T>G upstream_gene_variant 0.42
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.53
mmpR5 779048 p.Val20Ala missense_variant 0.42
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472512 n.667A>G non_coding_transcript_exon_variant 0.23
inhA 1674952 p.Pro251Ala missense_variant 0.35
rpsA 1834177 c.636A>C synonymous_variant 0.48
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155653 p.Lys153Asn missense_variant 0.46
katG 2155724 p.Ala130Thr missense_variant 0.45
PPE35 2167926 p.Leu896Ser missense_variant 0.94
PPE35 2169320 p.Leu431Phe missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.21
pncA 2289365 c.-125delC upstream_gene_variant 0.47
eis 2715579 c.-247G>C upstream_gene_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 0.48
pepQ 2860572 c.-154G>A upstream_gene_variant 0.45
Rv2752c 3065080 p.His371Arg missense_variant 0.12
Rv2752c 3066319 c.-128T>C upstream_gene_variant 0.33
thyA 3073806 c.666C>G synonymous_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474243 c.237C>T synonymous_variant 0.43
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63
clpC1 4039932 p.Gly258Val missense_variant 0.26
embC 4242075 p.Arg738Gln missense_variant 0.38
embC 4242476 p.Pro872Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.35
embA 4243460 c.228C>T synonymous_variant 0.61
embB 4249757 p.Thr1082Ala missense_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 0.48
aftB 4269564 c.-728G>A upstream_gene_variant 0.53
ethA 4327132 p.Asn114Lys missense_variant 0.36
whiB6 4338286 c.235delG frameshift_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.45
gid 4408018 p.Gly62Val missense_variant 0.57
gid 4408168 p.Phe12Cys missense_variant 0.4