TB-Profiler result

Run: SRR6797496
Summary

Run ID: SRR6797496

Sample name:

Date: 04-04-2023 16:11:08

Number of reads: 887411

Percentage reads mapped: 99.49

Strain: lineage3

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
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 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155720 c.390_391delGC frameshift_variant 1.0 isoniazid, isoniazid
embB 4247429 p.Met306Val 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9749 c.2448G>C synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762121 p.Asp772Gly 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 767058 p.Thr1230Asn missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779613 c.-708C>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304381 p.Ala484Val missense_variant 0.11
Rv1258c 1406665 p.Arg226Cys missense_variant 0.15
Rv1258c 1406868 p.Pro158Gln missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471911 n.66C>A non_coding_transcript_exon_variant 1.0
rrl 1475422 n.1765A>C non_coding_transcript_exon_variant 1.0
inhA 1674984 c.783C>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102826 p.Arg73Trp missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.42
Rv1979c 2221731 c.1434G>T synonymous_variant 0.12
Rv1979c 2223216 c.-52C>A upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.95
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747103 p.Ala166Pro missense_variant 0.15
pepQ 2860415 p.Thr2Ala missense_variant 0.12
ribD 2987419 p.Gly194Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4240098 p.Ala79Val missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242167 p.Val769Met missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245833 c.-681G>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
ubiA 4269918 c.-85G>A upstream_gene_variant 0.13
ethA 4327139 p.Ala112Gly missense_variant 1.0
whiB6 4338440 c.81dupT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407794 p.Arg137Gly missense_variant 1.0