TB-Profiler result

Run: ERR552562
Summary

Run ID: ERR552562

Sample name:

Date: 15-08-2022 10:51:31

Number of reads: 388863

Percentage reads mapped: 99.39

Strain: lineage1.2.2.1

Drug-resistance: Other

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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 0.99
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 Indo-Oceanic NA 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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 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
gyrA 9522 p.Pro741Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620128 p.Gly80Trp missense_variant 0.12
rpoB 759750 c.-57G>T upstream_gene_variant 0.12
rpoB 760124 c.318C>T synonymous_variant 1.0
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 766842 p.Val1158Asp missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781592 c.33T>A synonymous_variant 0.13
fbiC 1303675 p.Gly249Ser missense_variant 0.12
Rv1258c 1407278 c.63G>T synonymous_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472728 n.883G>A non_coding_transcript_exon_variant 1.0
rpsA 1834957 c.1416C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102802 p.Asn81Tyr missense_variant 0.13
katG 2153987 p.Glu709Lys missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154893 p.Glu407Lys missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222183 c.976_981dupCTTTGG conservative_inframe_insertion 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
kasA 2519341 c.1227G>A synonymous_variant 1.0
kasA 2519353 p.Phe413Leu missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3067155 c.-964C>T upstream_gene_variant 0.12
thyA 3074018 p.Phe152Leu missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087895 c.1081delG frameshift_variant 0.5
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449329 p.Arg276Cys missense_variant 0.13
fprA 3473826 c.-181C>T upstream_gene_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 3641298 c.-237G>A upstream_gene_variant 1.0
fbiB 3642518 c.984C>T synonymous_variant 1.0
ddn 3987145 p.Gln101Pro missense_variant 0.11
clpC1 4040241 p.Thr155Phe missense_variant 0.12
clpC1 4040250 p.Glu152Gly missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240731 p.Asn290Ile missense_variant 0.12
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4240997 p.Trp379Arg missense_variant 0.13
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242662 p.Ser934Pro missense_variant 0.11
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246661 p.Val50Met missense_variant 0.2
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 4326439 p.Asn345Lys missense_variant 0.97
ethA 4326714 p.Gln254Glu 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