TB-Profiler result

Run: SRR5153855
Summary

Run ID: SRR5153855

Sample name:

Date: 04-04-2023 09:27:12

Number of reads: 8438657

Percentage reads mapped: 99.44

Strain: lineage4.2.1;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
lineage2 East-Asian Beijing RD105 0.56
lineage4 Euro-American LAM;T;S;X;H None 0.46
lineage4.2 Euro-American H;T;LAM None 0.47
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.57
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.52
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.45
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
gyrA 7582 p.Asp94Gly missense_variant 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.57 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.46 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.37 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 0.29 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.13 kanamycin
embA 4243217 c.-16C>T upstream_gene_variant 0.16 ethambutol
embB 4247402 p.Ser297Ala missense_variant 0.14 ethambutol
embB 4247429 p.Met306Val missense_variant 0.51 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.37 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.39 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 0.46
fgd1 491742 c.960T>C synonymous_variant 0.54
mshA 575907 p.Ala187Val missense_variant 0.62
ccsA 619969 p.Val27Ile missense_variant 0.49
ccsA 620625 p.Ile245Met missense_variant 0.51
rpoB 761528 p.Asp574Glu missense_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 0.59
rpoC 764888 p.Leu507Val missense_variant 0.3
rpoC 766645 p.Glu1092Asp missense_variant 0.53
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776182 p.Asp767Asn missense_variant 0.55
mmpS5 779615 c.-710C>G upstream_gene_variant 0.59
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 0.34
Rv1258c 1406760 c.580_581insC frameshift_variant 0.58
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.47
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.56
PPE35 2167926 p.Leu896Ser missense_variant 0.58
PPE35 2169879 p.Phe245Cys missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
ribD 2986827 c.-12G>A upstream_gene_variant 0.38
Rv2752c 3064700 p.Ser498Pro missense_variant 0.58
ald 3086742 c.-78A>C upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.53
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.57
embB 4249594 c.3081G>A synonymous_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 0.51
ethA 4326632 p.His281Pro missense_variant 0.14
ethA 4328376 c.-903G>C upstream_gene_variant 0.38
whiB6 4338298 p.Leu75Gln missense_variant 0.61
whiB6 4338563 c.-42G>T upstream_gene_variant 0.66
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.53
gid 4407927 p.Glu92Asp missense_variant 0.53