TB-Profiler result

Run: SRR11972209
Summary

Run ID: SRR11972209

Sample name:

Date: 03-04-2023 05:32:08

Number of reads: 218527

Percentage reads mapped: 99.02

Strain: lineage1.1.1

Drug-resistance: MDR-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 0.95
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247469 p.Tyr319Cys missense_variant 1.0 ethambutol
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 5994 p.His252Arg missense_variant 0.13
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 9600 p.Ile767Val missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760321 p.Gln172Leu missense_variant 0.17
rpoB 761770 p.Met655Thr missense_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 765171 p.Pro601Leu missense_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 1302785 c.-146A>G upstream_gene_variant 1.0
fbiC 1304126 p.Val399Ala missense_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rpsA 1834315 c.774C>T synonymous_variant 1.0
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103022 c.21C>G synonymous_variant 1.0
katG 2154410 p.Thr568Ala missense_variant 0.17
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 2168253 p.Pro787Leu missense_variant 0.22
PPE35 2169574 p.Phe347Ile missense_variant 0.2
PPE35 2169902 c.711G>C synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222708 p.Leu153Phe missense_variant 0.4
Rv1979c 2222726 p.Val147Met missense_variant 0.5
Rv1979c 2223144 p.Arg7Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.94
kasA 2518123 c.9G>A synonymous_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065566 p.Pro209Leu missense_variant 0.18
Rv2752c 3067126 c.-935C>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086954 c.135C>T synonymous_variant 1.0
ald 3087373 p.Arg185His missense_variant 0.13
Rv3083 3448312 c.-192T>A upstream_gene_variant 0.33
Rv3083 3448314 c.-190C>G upstream_gene_variant 0.33
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
Rv3236c 3612538 c.579T>A synonymous_variant 0.29
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3987117 p.Leu92Phe missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 0.89
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
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 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248345 c.1834delG frameshift_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 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
gid 4407979 p.Pro75Leu missense_variant 1.0