TB-Profiler result

Run: SRR1144804
Summary

Run ID: SRR1144804

Sample name:

Date: 02-04-2023 21:13:35

Number of reads: 655593

Percentage reads mapped: 99.4

Strain: lineage4;lineage2.2

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
lineage2 East-Asian Beijing RD105 0.11
lineage4 Euro-American LAM;T;S;X;H None 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.18
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 761004 p.Thr400Ala missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.22 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.81 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 0.23 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.78 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288887 p.Trp119Gly missense_variant 0.75 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.25 ethambutol
ethA 4326505 c.966_968dupGAC disruptive_inframe_insertion 0.6 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 0.29
mshA 576293 p.Ala316Ser missense_variant 0.29
rpoB 761889 p.Val695Leu missense_variant 0.63
rpoC 763031 c.-339T>C upstream_gene_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.29
mmpL5 777875 c.605delG frameshift_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.73
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474344 n.688delA non_coding_transcript_exon_variant 0.12
rrl 1474347 n.690T>C non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.17
rpsA 1834776 p.Ala412Val missense_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101831 c.1212G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.31
katG 2156173 c.-62C>A upstream_gene_variant 0.84
PPE35 2167926 p.Leu896Ser missense_variant 0.13
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726141 c.-52C>A upstream_gene_variant 0.64
Rv2752c 3065314 c.875_877dupCCG conservative_inframe_insertion 0.14
Rv2752c 3065517 c.675C>T synonymous_variant 0.9
thyA 3074495 c.-24C>T upstream_gene_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 0.33
Rv3083 3448331 c.-173_-172insCGC upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.27
fprA 3474299 p.Asp98Gly missense_variant 0.73
Rv3236c 3612219 p.Val300Ile missense_variant 0.83
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11
fbiB 3640879 c.-656C>T upstream_gene_variant 0.37
alr 3840970 c.447_450dupCCGG frameshift_variant 0.18
rpoA 3878635 c.-128C>T upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243598 c.366G>A synonymous_variant 0.5
ethA 4326474 p.Pro334Ala missense_variant 0.43
ethA 4328317 c.-844C>T upstream_gene_variant 0.8
whiB6 4338326 p.Ala66Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.11
gid 4407967 p.Leu79Trp missense_variant 0.96