TB-Profiler result

Run: SRR22175229
Summary

Run ID: SRR22175229

Sample name:

Date: 04-04-2023 04:02:10

Number of reads: 1698993

Percentage reads mapped: 99.14

Strain: lineage4.2.2.2

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
lineage4.2 Euro-American H;T;LAM None 0.96
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.96
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 761101 p.Gln432Pro missense_variant 1.0 rifampicin
katG 2155167 p.Ser315Thr missense_variant 0.79 isoniazid
pncA 2288945 c.284_296delACAAGGGTGCCTA frameshift_variant 0.96 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.52 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.42 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 8688 p.Ala463Ser missense_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 761547 p.Val581Leu 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 1471972 n.127T>C non_coding_transcript_exon_variant 0.1
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.13
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.12
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.11
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.12
rrl 1475387 n.1730C>T non_coding_transcript_exon_variant 0.94
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.1
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.11
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.11
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.11
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.1
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.12
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.13
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.11
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.11
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.12
rrl 1476113 n.2456T>G non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
rpsA 1833585 p.Asp15Gly missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.96
ald 3086742 c.-78A>C upstream_gene_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474755 p.Lys250Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242689 p.Val943Ile missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0