TB-Profiler result

Run: ERR2514808
Summary

Run ID: ERR2514808

Sample name:

Date: 31-03-2023 20:34:41

Number of reads: 3131172

Percentage reads mapped: 99.17

Strain: lineage1.2.2

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_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 9020 c.1719G>A synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490693 c.-90G>T upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576653 p.Ala436Thr missense_variant 0.29
mshA 576768 p.Pro474Leu missense_variant 0.2
ccsA 620045 p.Gly52Glu missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763690 c.321C>T synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304226 c.1296C>T synonymous_variant 0.5
fbiC 1304311 p.Ala461Ser missense_variant 0.15
fbiC 1304488 p.Ala520Thr missense_variant 0.14
Rv1258c 1407146 c.195G>A synonymous_variant 0.5
Rv1258c 1407158 c.183C>A synonymous_variant 0.4
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155726 p.Phe129Ser missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860111 p.Thr103Met missense_variant 0.15
thyX 3067349 c.597G>T synonymous_variant 0.5
thyX 3067379 p.Tyr189* stop_gained 0.25
thyX 3067571 p.Asp125Glu missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
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
fbiB 3641892 c.358C>T synonymous_variant 0.18
fbiB 3641994 p.Arg154Cys missense_variant 1.0
fbiB 3642012 p.Gln160* stop_gained 0.5
fbiB 3642132 p.Ala200Thr missense_variant 0.5
clpC1 4040517 p.Val63Ala missense_variant 0.99
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.95
embA 4242310 c.-923C>T upstream_gene_variant 0.12
embA 4242583 c.-650C>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244304 c.1072C>A synonymous_variant 0.29
embA 4244403 p.Val391Ile missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246782 p.Ala90Asp missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327791 c.-318A>G upstream_gene_variant 1.0
whiB6 4338179 p.Ser115Ala missense_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0