TB-Profiler result

Run: SRR22175232
Summary

Run ID: SRR22175232

Sample name:

Date: 04-04-2023 04:02:10

Number of reads: 1099956

Percentage reads mapped: 99.26

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.99
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.97
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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9323 c.2022C>G synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761534 c.1728G>A synonymous_variant 0.14
rpoB 761933 c.2127G>T synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762923 c.-447C>G upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
mmpS5 778835 p.Thr24Met missense_variant 1.0
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473335 n.1490G>A non_coding_transcript_exon_variant 0.17
rrl 1474484 n.827C>G non_coding_transcript_exon_variant 0.11
rrl 1475496 n.1839C>A non_coding_transcript_exon_variant 0.13
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.96
PPE35 2168465 c.2148C>A synonymous_variant 0.12
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518247 p.Ala45Pro missense_variant 0.91
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4040836 c.-132T>C upstream_gene_variant 0.12
embC 4241170 c.1308G>A synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248901 p.His796Gln missense_variant 0.11
ubiA 4269875 c.-42G>A upstream_gene_variant 1.0
ethA 4326620 p.His285Pro missense_variant 0.93
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0