TB-Profiler result

Run: SRR1172749
Summary

Run ID: SRR1172749

Sample name:

Date: 03-04-2023 03:09:47

Number of reads: 615735

Percentage reads mapped: 91.13

Strain: lineage4.8.1

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.98
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
gyrB 6736 p.Asn499Lys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 1.0 pyrazinamide
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, 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
fgd1 490739 c.-44G>A upstream_gene_variant 0.22
fgd1 491416 c.635delG frameshift_variant 0.12
ccsA 620740 p.Thr284Ala missense_variant 0.13
rpoB 760322 p.Gln172His missense_variant 0.15
rpoB 760685 p.Leu293Phe missense_variant 0.12
rpoC 765287 p.Leu640Met missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417143 p.Arg69Cys missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168786 c.1827G>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715433 c.-101T>C upstream_gene_variant 0.18
Rv2752c 3065329 p.Asp288Val missense_variant 0.13
ald 3087128 p.Cys103* stop_gained 0.12
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
fbiB 3642874 p.Leu447Arg missense_variant 1.0
clpC1 4038254 c.2451G>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269307 p.Phe176Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0