TB-Profiler result

Run: SRR998857
Summary

Run ID: SRR998857

Sample name:

Date: 04-04-2023 23:39:10

Number of reads: 1021730

Percentage reads mapped: 99.42

Strain: lineage4.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288766 p.Leu159Arg missense_variant 0.94 pyrazinamide
ethA 4326352 c.1120_1121delCT frameshift_variant 1.0 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 491247 c.465C>T synonymous_variant 0.93
mshA 576265 c.918G>T synonymous_variant 0.11
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155773 c.339C>T synonymous_variant 0.11
PPE35 2167745 p.Thr956Arg missense_variant 0.12
PPE35 2169695 c.918A>G synonymous_variant 0.11
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.98
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640439 c.-104C>A upstream_gene_variant 1.0
alr 3841356 p.Ser22Leu missense_variant 1.0
rpoA 3878655 c.-148C>A upstream_gene_variant 0.22
panD 4044207 c.75G>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>T upstream_gene_variant 1.0
embB 4247709 p.Asn399Thr missense_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0