TB-Profiler result

Run: SRR7517715
Summary

Run ID: SRR7517715

Sample name:

Date: 04-04-2023 19:33:32

Number of reads: 1195613

Percentage reads mapped: 96.82

Strain: lineage1.1.1.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.99
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6493 c.-809C>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620754 c.864G>T synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765544 c.2175C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1475681 n.2024C>T non_coding_transcript_exon_variant 0.4
inhA 1674469 p.Gly90Trp missense_variant 0.17
rpsA 1834319 p.Val260Ile missense_variant 1.0
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168291 p.Leu774Phe missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.14
kasA 2518609 p.Met165Ile missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94
ahpC 2726363 p.Phe57Leu missense_variant 0.4
folC 2746530 p.Ala357Ser missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3841492 c.-72C>T upstream_gene_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038596 c.2109A>G synonymous_variant 0.18
clpC1 4040483 c.222G>A synonymous_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4244816 c.1584G>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246528 c.15G>T synonymous_variant 0.24
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267953 p.Ala295Glu missense_variant 0.15
aftB 4268798 c.39C>A synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326340 c.1134C>A synonymous_variant 0.22
ethA 4327551 c.-78C>A upstream_gene_variant 0.2
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338582 c.-61G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407636 c.567G>T synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408087 c.115dupC frameshift_variant 1.0