TB-Profiler result

Run: ERR2514920
Summary

Run ID: ERR2514920

Sample name:

Date: 31-03-2023 20:38:35

Number of reads: 514613

Percentage reads mapped: 96.61

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575433 p.Gly29Asp missense_variant 0.17
mshA 575920 c.573C>T synonymous_variant 0.33
ccsA 619904 p.His5Arg missense_variant 0.25
ccsA 620701 p.Ala271Thr missense_variant 0.2
rpoB 759620 c.-187A>C upstream_gene_variant 0.38
rpoB 761219 c.1413G>T synonymous_variant 0.13
rpoB 761771 p.Met655Ile missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764653 c.1284G>A synonymous_variant 0.17
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777001 p.His494Tyr missense_variant 0.22
mmpL5 777026 c.1455C>T synonymous_variant 0.22
mmpL5 777760 p.Leu241Phe missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781887 p.Arg110Cys missense_variant 0.11
rplC 800711 c.-98C>T upstream_gene_variant 0.14
fbiC 1303016 p.Val29Gly missense_variant 0.27
Rv1258c 1407377 c.-37C>A upstream_gene_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417176 p.Ala58Ser missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834195 c.654G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101701 c.1342C>T synonymous_variant 0.22
ndh 2103225 c.-183A>C upstream_gene_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168904 p.Ile570Thr missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289922 c.-681C>T upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714147 p.Val396Ile missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726612 c.420C>T synonymous_variant 0.13
folC 2747639 c.-41C>G upstream_gene_variant 0.25
pepQ 2860161 c.258G>A synonymous_variant 0.12
ribD 2987000 c.162C>G synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065655 c.537C>T synonymous_variant 1.0
Rv2752c 3065784 c.408C>T synonymous_variant 0.17
Rv2752c 3066383 c.-192T>C upstream_gene_variant 0.2
thyA 3074256 c.216G>T synonymous_variant 0.22
ald 3086667 c.-153_-152insG upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087378 p.Ala187Thr missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568507 p.Gln58Arg missense_variant 1.0
whiB7 3568593 c.87C>T synonymous_variant 0.17
fbiA 3640389 c.-154C>A upstream_gene_variant 0.14
fbiB 3640545 c.-990G>A upstream_gene_variant 0.14
fbiB 3642362 c.828C>T synonymous_variant 0.2
alr 3840328 c.1093T>C synonymous_variant 0.14
clpC1 4038475 p.Ser744Gly missense_variant 0.22
clpC1 4040217 p.Gly163Val missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4043974 p.Pro103Leu missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241095 c.1233C>T synonymous_variant 0.17
embC 4242614 p.Ala918Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243822 p.Thr197Met missense_variant 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248241 c.1728C>A synonymous_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327197 p.Gly93Arg missense_variant 0.25
ethA 4328001 c.-528G>A upstream_gene_variant 0.12
whiB6 4338441 p.Tyr27* stop_gained 0.71
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338702 c.-181T>A upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408050 c.152delA frameshift_variant 0.2