TB-Profiler result

Run: SRR12830390
Summary

Run ID: SRR12830390

Sample name:

Date: 03-04-2023 06:59:01

Number of reads: 482149

Percentage reads mapped: 99.86

Strain: lineage4.3.4.2

Drug-resistance: Sensitive

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
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 6160 c.921C>T synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761094 p.Leu430Met missense_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765865 c.2496C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778511 c.394delG frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800753 c.-56C>A upstream_gene_variant 0.14
embR 1416943 p.Ser135Arg missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473941 n.289_302dupAACCGGGTAGGGGT non_coding_transcript_exon_variant 0.4
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.2
rrl 1475300 n.1643G>T non_coding_transcript_exon_variant 0.18
rrl 1475403 n.1746T>C non_coding_transcript_exon_variant 0.25
fabG1 1673521 p.Gly28Trp missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154029 p.Asp695Tyr missense_variant 0.12
katG 2154383 p.Glu577* stop_gained 0.18
PPE35 2170546 p.Pro23Ser missense_variant 0.14
PPE35 2170651 c.-39T>C upstream_gene_variant 0.18
Rv1979c 2222379 c.786G>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518017 c.-98G>A upstream_gene_variant 0.12
ahpC 2726113 c.-80A>G upstream_gene_variant 0.18
ribD 2986769 c.-70C>A upstream_gene_variant 0.12
ribD 2986883 p.Arg15Ser missense_variant 0.12
ribD 2987310 p.Gly158Arg missense_variant 0.1
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3877797 c.711G>T synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247884 c.1371C>A synonymous_variant 1.0
embB 4249414 c.2901G>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0