TB-Profiler result

Run: SRR19428627
Summary

Run ID: SRR19428627

Sample name:

Date: 03-04-2023 21:42:51

Number of reads: 272589

Percentage reads mapped: 99.82

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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8661 p.Asp454Tyr missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490650 c.-133G>T upstream_gene_variant 0.18
mshA 575379 p.Gly11Val missense_variant 0.15
mshA 575552 p.Asn69Asp missense_variant 0.11
mshA 576781 c.1434G>T synonymous_variant 0.25
rpoB 760117 p.Pro104His missense_variant 0.12
rpoB 760478 c.672C>T synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776185 p.Lys766* stop_gained 0.14
mmpS5 779588 c.-683C>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304242 p.Pro438Ser missense_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473376 n.1531C>A non_coding_transcript_exon_variant 0.14
rrl 1475829 n.2172C>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154051 c.2061G>T synonymous_variant 0.14
PPE35 2167837 p.Gly926Trp missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747319 p.Gly94Cys missense_variant 0.22
pepQ 2859335 c.1084T>C synonymous_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339708 c.591C>A synonymous_variant 0.17
Rv3083 3449728 p.Leu409Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3613142 c.-26A>T upstream_gene_variant 0.13
alr 3840412 p.Gly337Cys missense_variant 0.14
rpoA 3877977 p.Lys177Asn missense_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040360 p.Glu115Asp missense_variant 0.12
embC 4239871 c.9C>A synonymous_variant 0.15
embC 4239887 p.Arg9Ser missense_variant 0.14
embC 4241086 c.1224G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246830 p.Gly106Val missense_variant 0.14
embB 4246941 p.Pro143Arg missense_variant 1.0
embB 4249316 p.Ala935Ser missense_variant 0.5
aftB 4266966 p.Pro624Leu missense_variant 0.13
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0