TB-Profiler result

Run: SRR671760

Summary

Run ID: SRR671760

Sample name:

Date: 12-08-2022 03:48:17

Number of reads: 5509686

Percentage reads mapped: 99.51

Strain: lineage4.4.2

Drug-resistance: Pre-XDR-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
lineage4.4.2 Euro-American T1;T2 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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2154857 p.Asp419His missense_variant 1.0 isoniazid
pncA 2288965 c.272_276delAGGCG frameshift_variant 1.0 pyrazinamide
eis 2715339 c.-8delC upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326853 c.620dupG 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
gyrB 6639 p.Ala467Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.23
rpoC 767118 p.Glu1250Ala missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
pepQ 2859381 c.1038C>G synonymous_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.22
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.13
thyA 3074176 p.Arg99Gln missense_variant 0.23
thyA 3074282 p.Arg64Cys missense_variant 0.39
thyA 3074283 p.Leu63Phe missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.16
clpC1 4039932 p.Gly258Val missense_variant 0.15
clpC1 4040102 p.Met201Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.38
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0