TB-Profiler result

Run: SRR21676316
Summary

Run ID: SRR21676316

Sample name:

Date: 04-04-2023 02:41:30

Number of reads: 336321

Percentage reads mapped: 99.51

Strain: lineage4.3.2

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
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 6982 c.-320A>G upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7720 p.Glu140Val missense_variant 0.2
gyrA 8301 p.His334Tyr missense_variant 0.1
gyrA 8999 p.Leu566Phe missense_variant 0.14
gyrA 9113 c.1812C>A synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.45
mshA 575821 c.474G>T synonymous_variant 0.25
ccsA 620698 p.Val270Leu missense_variant 0.18
rpoB 759620 c.-187A>C upstream_gene_variant 0.18
rpoB 760253 c.447T>C synonymous_variant 0.11
rpoB 760442 p.Lys212Asn missense_variant 0.12
rpoB 762033 p.Ser743Thr missense_variant 0.14
rpoB 762139 p.Leu778Gln missense_variant 0.29
rpoC 762950 c.-420G>A upstream_gene_variant 0.4
rpoC 764344 c.975C>A synonymous_variant 0.15
rpoC 764911 c.1542A>G synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766715 p.Ala1116Ser missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775809 p.Thr891Asn missense_variant 0.11
mmpL5 776134 p.Ala783Thr missense_variant 0.11
mmpL5 777119 p.His454Gln missense_variant 0.12
mmpL5 777122 c.1359C>T synonymous_variant 0.12
mmpL5 777128 c.1353A>G synonymous_variant 0.12
mmpL5 777527 c.954G>T synonymous_variant 0.18
mmpS5 778607 p.Ala100Asp missense_variant 0.22
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.22
mmpS5 778630 p.Leu92Phe missense_variant 0.22
mmpS5 778632 c.267_273delGCTCACC frameshift_variant 0.29
mmpR5 779383 p.Arg132Gly missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781427 c.-133G>A upstream_gene_variant 0.2
fbiC 1303995 c.1065C>T synonymous_variant 0.2
fbiC 1304023 p.Val365Ile missense_variant 0.15
embR 1416376 c.972C>T synonymous_variant 0.13
atpE 1461005 c.-40G>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473514 n.-144C>A upstream_gene_variant 0.11
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102368 c.675C>A synonymous_variant 0.15
katG 2154109 p.Trp668Leu missense_variant 0.12
katG 2155043 p.Asp357Tyr missense_variant 0.14
katG 2156025 c.87C>A synonymous_variant 0.1
katG 2156361 c.-250G>A upstream_gene_variant 0.18
PPE35 2168810 c.1803T>C synonymous_variant 0.12
Rv1979c 2222436 c.729A>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289526 c.-285T>G upstream_gene_variant 0.18
kasA 2518196 p.Asp28Tyr missense_variant 0.2
pepQ 2860279 p.Ala47Asp missense_variant 0.15
Rv2752c 3066082 p.Leu37Pro missense_variant 0.22
Rv2752c 3066194 c.-3G>A upstream_gene_variant 0.2
Rv2752c 3066391 c.-200C>T upstream_gene_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074004 c.468T>C synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087836 c.1017A>G synonymous_variant 0.14
Rv3083 3448835 p.Ser111Asn missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474558 c.552A>G synonymous_variant 0.13
Rv3236c 3612682 p.Asn145Lys missense_variant 0.15
fbiB 3641624 c.90C>T synonymous_variant 0.29
rpoA 3877630 p.Ser293Tyr missense_variant 0.14
rpoA 3878567 c.-60C>G upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039484 c.1221T>G synonymous_variant 0.33
clpC1 4039487 c.1217delC frameshift_variant 0.17
panD 4043889 c.393G>A synonymous_variant 1.0
embC 4240371 p.Gly170Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243232 c.-1C>T upstream_gene_variant 0.25
embA 4243840 p.Lys203Arg missense_variant 0.25
embB 4247017 c.504G>T synonymous_variant 0.29
embB 4247059 c.546C>G synonymous_variant 0.2
embB 4247060 p.Pro183Ala missense_variant 0.2
embB 4247066 p.Ile185Val missense_variant 0.2
embB 4247174 p.Ala221Thr missense_variant 0.2
embB 4248087 p.Tyr525Ser missense_variant 0.25
ethR 4327587 p.Arg13Ser missense_variant 0.17
ethR 4328083 p.Asn179Asp missense_variant 0.18
ethA 4328412 c.-939G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0