TB-Profiler result

Run: SRR6930916
Summary

Run ID: SRR6930916

Sample name:

Date: 04-04-2023 18:13:11

Number of reads: 2052229

Percentage reads mapped: 99.34

Strain: lineage4.8

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
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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
pncA 2289026 p.Cys72* stop_gained 1.0 pyrazinamide
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 8156 c.855T>G synonymous_variant 0.98
rpoC 765599 p.Glu744Lys missense_variant 0.99
rpoC 767302 c.3933C>T synonymous_variant 1.0
mmpL5 775609 p.Ala958Thr missense_variant 1.0
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
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.99
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155995 p.Trp39* stop_gained 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170456 p.Val53Ile missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074369 p.Arg35Cys missense_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4242083 c.2221C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4247829 p.Ala439Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408048 p.Cys52Tyr missense_variant 0.98
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0