TB-Profiler result

Run: SRR9588022
Summary

Run ID: SRR9588022

Sample name:

Date: 02-08-2023 15:35:04

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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 761076 p.Phe424Leu missense_variant 0.15 rifampicin
rpoB 761086 p.Thr427Ile missense_variant 0.2 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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
gyrB 6053 p.His272Tyr missense_variant 0.11
gyrB 6406 p.Asn389Lys missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9534 c.2238_2240delCGG disruptive_inframe_deletion 0.12
rpoC 763627 p.Lys86Asn missense_variant 0.1
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpR5 779360 p.Ala124Glu missense_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781899 p.Arg114Cys missense_variant 0.12
Rv1258c 1407217 p.Gly42Trp missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475635 n.1978G>T non_coding_transcript_exon_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
inhA 1674605 p.Leu135Gln missense_variant 0.14
rpsA 1834753 c.1212T>C synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289860 c.-619A>G upstream_gene_variant 0.13
kasA 2518496 c.382C>T synonymous_variant 1.0
kasA 2518765 c.651G>A synonymous_variant 0.12
folC 2747450 p.Ile50Thr missense_variant 0.11
Rv2752c 3065023 p.Pro390Leu missense_variant 1.0
thyX 3067645 p.Tyr101His missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448522 p.Val7Phe missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475339 p.Ala445Ser missense_variant 0.22
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642198 p.Val222Met missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0