TB-Profiler result

Run: SRR11972202
Summary

Run ID: SRR11972202

Sample name:

Date: 03-04-2023 05:31:53

Number of reads: 229732

Percentage reads mapped: 99.19

Strain: lineage1.1.1

Drug-resistance: HR-TB

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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 1.0
lineage1.1.1 Indo-Oceanic EAI4;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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
gid 4407851 c.351delG 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 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
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761770 p.Met655Thr missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763633 c.264T>A synonymous_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 0.33
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766342 c.2973C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 779254 c.-774G>T upstream_gene_variant 0.29
mmpS5 779658 c.-753T>C upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302785 c.-146A>G upstream_gene_variant 1.0
fbiC 1303913 p.Gly328Asp missense_variant 0.12
fbiC 1305323 p.Val798Ala missense_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472025 n.180A>T non_coding_transcript_exon_variant 0.15
rrs 1472295 n.450A>T non_coding_transcript_exon_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
fabG1 1673641 p.Val68Ile missense_variant 0.25
rpsA 1833436 c.-106C>A upstream_gene_variant 0.13
rpsA 1834315 c.774C>T synonymous_variant 1.0
rpsA 1834319 p.Val260Ile missense_variant 1.0
rpsA 1834736 c.1198delA frameshift_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101813 c.1230G>A synonymous_variant 1.0
ndh 2103022 c.21C>G synonymous_variant 1.0
katG 2153947 p.Gln722Leu missense_variant 0.25
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 2169024 p.Pro530Leu missense_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170271 c.342T>C synonymous_variant 0.14
PPE35 2170280 c.333C>G synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223144 p.Arg7Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518123 c.9G>A synonymous_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714443 p.Arg297His missense_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074224 p.Trp83Leu missense_variant 0.25
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
whiB7 3568426 p.Arg85His missense_variant 0.18
fbiA 3640768 p.Gln76* stop_gained 0.17
fbiA 3641134 p.Glu198Lys missense_variant 0.25
alr 3840923 c.498C>A synonymous_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3986932 p.Arg30His missense_variant 0.15
clpC1 4040097 p.Val203Glu missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242177 p.Pro772Leu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243720 p.Pro163Leu missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4244965 p.Ala578Val missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247558 p.Trp349Arg missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267574 c.1263G>A synonymous_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338329 p.Asp65Asn missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338662 c.-141G>T upstream_gene_variant 0.13
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0