TB-Profiler result

Run: SRR3082069
Summary

Run ID: SRR3082069

Sample name:

Date: 04-04-2023 04:52:35

Number of reads: 1121272

Percentage reads mapped: 96.85

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7850 c.549C>G synonymous_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8877 p.Ala526Thr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761775 p.Asp657Asn missense_variant 0.12
rpoC 763543 p.Trp58* stop_gained 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779379 c.-899C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303609 p.Gly227Arg missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.1
rrl 1476116 n.2459A>G non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167979 c.2634A>G synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.17
PPE35 2170066 p.Ala183Thr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289480 c.-239G>A upstream_gene_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3064545 c.1647G>T synonymous_variant 0.17
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyX 3067579 p.Glu123Gln missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339402 c.285C>T synonymous_variant 0.13
Rv3083 3449105 p.Pro201Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612098 p.Ile340Thr missense_variant 0.1
alr 3840850 c.571C>A synonymous_variant 1.0
rpoA 3877664 p.Asp282Asn missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039111 c.1593delC frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244860 p.Gly543Glu missense_variant 0.11
embB 4247484 p.Gly324Val missense_variant 0.13
aftB 4268712 p.Leu42* stop_gained 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407620 p.Tyr195Asn missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0