TB-Profiler result

Run: SRR12199470
Summary

Run ID: SRR12199470

Sample name:

Date: 03-04-2023 06:42:23

Number of reads: 356291

Percentage reads mapped: 86.23

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 5409 p.Ala57Val missense_variant 0.13
gyrB 5676 p.Trp146Leu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575799 p.Val151Ala missense_variant 1.0
ccsA 620466 c.576C>A synonymous_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761966 p.Trp720Cys missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767206 c.3837C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776612 c.1869C>T synonymous_variant 0.17
mmpL5 776967 p.Gly505Val missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781449 c.-111G>T upstream_gene_variant 0.18
rpsL 781806 p.Arg83Cys missense_variant 0.14
fbiC 1302995 p.Asn22Ile missense_variant 0.2
embR 1416569 p.Leu260Pro missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 0.95
rrs 1472236 n.391C>T non_coding_transcript_exon_variant 0.12
fabG1 1673326 c.-114C>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155519 p.Trp198Leu missense_variant 0.2
katG 2156344 c.-233C>A upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.18
PPE35 2169695 c.918A>G synonymous_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.83
PPE35 2170053 p.Thr187Ser missense_variant 0.83
PPE35 2170147 p.Ser156Ala missense_variant 0.27
PPE35 2170473 p.Ser47Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289257 c.-16A>T upstream_gene_variant 0.2
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518516 c.402C>T synonymous_variant 0.25
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.43
ahpC 2726515 p.Phe108Ser missense_variant 0.2
Rv2752c 3066080 p.Gly38Cys missense_variant 0.2
Rv2752c 3066211 c.-20A>G upstream_gene_variant 0.18
thyX 3067673 p.His91Gln missense_variant 0.2
thyX 3068096 c.-151A>G upstream_gene_variant 0.29
thyA 3074648 c.-177T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.4
fbiD 3339668 p.Gly184Val missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841521 c.-101G>T upstream_gene_variant 0.14
alr 3841546 c.-126C>A upstream_gene_variant 0.28
clpC1 4040082 p.Thr208Ile missense_variant 1.0
embC 4239721 c.-142C>T upstream_gene_variant 0.22
embC 4241610 p.Pro583Gln missense_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245404 c.2172C>T synonymous_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4249250 p.Ala913Ser missense_variant 0.5
embB 4249588 c.3075C>T synonymous_variant 0.22
aftB 4267342 p.Gly499Trp missense_variant 0.18
ubiA 4269158 p.Ala226Thr missense_variant 0.18
ethA 4327119 p.His119Tyr missense_variant 1.0
ethR 4327243 c.-306G>A upstream_gene_variant 0.4
ethA 4327749 c.-276G>T upstream_gene_variant 0.17
ethA 4328281 c.-808C>A upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0