TB-Profiler result

Run: SRR19428612
Summary

Run ID: SRR19428612

Sample name:

Date: 03-04-2023 21:42:08

Number of reads: 69241

Percentage reads mapped: 99.85

Strain: lineage4.3.4

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 0.36
lineage4.3.4 Euro-American (LAM) LAM 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 6439 c.-863C>A upstream_gene_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7966 p.Arg222Gln missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575770 c.423G>T synonymous_variant 0.22
ccsA 619963 p.Leu25Met missense_variant 0.5
ccsA 620271 c.381C>A synonymous_variant 0.5
ccsA 620285 p.Ala132Val missense_variant 0.5
ccsA 620678 p.Pro263His missense_variant 0.5
rpoB 761321 p.Phe505Leu missense_variant 0.18
rpoC 764636 p.Asp423Tyr missense_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766390 c.3021C>T synonymous_variant 1.0
rpoC 766466 p.Glu1033* stop_gained 0.33
rpoC 767149 c.3780C>T synonymous_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 p.Leu919Met missense_variant 0.5
mmpL5 776037 p.Ser815* stop_gained 0.4
mmpL5 776456 c.2025G>T synonymous_variant 0.4
mmpL5 778705 c.-225C>A upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305426 c.2496G>A synonymous_variant 0.29
embR 1416195 p.His385Tyr missense_variant 1.0
embR 1417425 c.-78C>A upstream_gene_variant 0.4
embR 1417536 c.-189C>A upstream_gene_variant 0.4
atpE 1461042 c.-3G>T upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471944 n.99G>T non_coding_transcript_exon_variant 0.29
rrs 1472915 n.1070G>T non_coding_transcript_exon_variant 0.25
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.33
rrl 1475933 n.2276C>A non_coding_transcript_exon_variant 0.29
rrl 1476370 n.2713C>T non_coding_transcript_exon_variant 0.29
rrl 1476675 n.3018C>A non_coding_transcript_exon_variant 0.22
rrl 1476761 n.3104G>A non_coding_transcript_exon_variant 0.29
inhA 1673685 c.-517C>A upstream_gene_variant 0.5
inhA 1673839 c.-363C>A upstream_gene_variant 0.4
inhA 1673967 c.-235G>T upstream_gene_variant 0.33
inhA 1674081 c.-121C>A upstream_gene_variant 0.5
inhA 1674949 p.Leu250Met missense_variant 0.67
tlyA 1917936 c.-4C>A upstream_gene_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102863 c.180C>A synonymous_variant 0.29
katG 2154077 p.Gln679Lys missense_variant 0.67
katG 2154396 c.1716G>T synonymous_variant 0.67
PPE35 2168438 c.2175C>A synonymous_variant 0.18
PPE35 2169021 p.Gly531Val missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288986 p.Asp86Tyr missense_variant 0.33
kasA 2519204 p.Asp364Tyr missense_variant 0.67
kasA 2519341 c.1227G>T synonymous_variant 0.4
eis 2714309 p.Pro342Thr missense_variant 0.5
pepQ 2860601 c.-183C>T upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3087669 p.Asp284Tyr missense_variant 0.67
Rv3083 3449406 c.903C>A synonymous_variant 0.29
Rv3083 3449562 c.1059G>T synonymous_variant 0.29
Rv3083 3449566 p.Gly355Trp missense_variant 0.29
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840625 p.Leu266Ile missense_variant 0.29
alr 3840691 p.Pro244Thr missense_variant 0.33
rpoA 3878146 p.Pro121His missense_variant 0.5
rpoA 3878268 c.240C>A synonymous_variant 0.4
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039074 p.Arg544Leu missense_variant 0.29
embC 4239715 c.-148G>T upstream_gene_variant 0.33
embC 4239967 c.105G>T synonymous_variant 0.5
embC 4241102 p.Glu414* stop_gained 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243366 p.Trp45Leu missense_variant 0.25
embA 4244144 p.Phe304Leu missense_variant 0.33
embA 4244225 c.993C>A synonymous_variant 0.5
embA 4245444 p.Asp738Tyr missense_variant 1.0
ubiA 4269707 p.Gly43Cys missense_variant 0.29
ethA 4326983 p.Pro164Gln missense_variant 0.25
ethA 4326989 p.Ile162Asn missense_variant 0.29
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
ethA 4328333 c.-860C>A upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0