TB-Profiler result

Run: SRR11972268
Summary

Run ID: SRR11972268

Sample name:

Date: 03-04-2023 05:34:09

Number of reads: 168184

Percentage reads mapped: 99.59

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 0.96
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 5488 c.249C>T synonymous_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7407 p.Ile36Phe missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7707 p.Pro136Ser missense_variant 0.33
gyrA 8546 c.1245T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491170 p.Ala130Thr missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762024 p.Val740Leu missense_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 763030 p.Ala1075Val missense_variant 0.2
rpoC 763858 c.489A>G synonymous_variant 0.18
rpoC 766711 c.3342C>G synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775659 c.2821delC frameshift_variant 0.22
mmpS5 779597 c.-693delA upstream_gene_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801311 p.Gly168Glu missense_variant 0.17
fbiC 1305369 c.2439G>A synonymous_variant 0.18
embR 1417065 p.Ala95Thr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472691 n.846G>A non_coding_transcript_exon_variant 0.22
rrs 1472729 n.884T>C non_coding_transcript_exon_variant 0.5
rrs 1472892 n.1047T>C non_coding_transcript_exon_variant 0.29
rrl 1473878 n.221A>T non_coding_transcript_exon_variant 0.2
rrl 1473962 n.305T>G non_coding_transcript_exon_variant 0.25
inhA 1673826 c.-376C>T upstream_gene_variant 0.22
inhA 1673967 c.-235G>A upstream_gene_variant 1.0
rpsA 1833421 c.-121C>T upstream_gene_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101763 p.Gly427Asp missense_variant 0.5
katG 2154540 c.1572C>A synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167916 c.2696delT frameshift_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168144 c.2469G>A synonymous_variant 0.33
PPE35 2169269 c.1344A>G synonymous_variant 0.29
PPE35 2169272 c.1341C>G synonymous_variant 0.29
PPE35 2170080 c.524_532delCGGCGGGTC disruptive_inframe_deletion 1.0
Rv1979c 2221765 p.Tyr467Ser missense_variant 0.4
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
eis 2714216 p.Asn373Asp missense_variant 0.14
eis 2714561 p.Gly258Cys missense_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726430 p.Ala80Thr missense_variant 1.0
folC 2746169 p.Ala477Val missense_variant 0.29
Rv2752c 3065468 p.Val242Met missense_variant 0.18
Rv2752c 3065693 p.His167Asn missense_variant 0.5
thyX 3067680 p.Cys89His missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087372 p.Arg185Ser missense_variant 0.33
fbiD 3339408 c.291C>T synonymous_variant 0.33
fbiD 3339575 p.Ala153Val missense_variant 0.33
Rv3083 3448556 p.Gly18Glu missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474043 p.Pro13Ser missense_variant 0.29
fprA 3474082 p.Ala26Thr missense_variant 0.29
whiB7 3568721 c.-42T>C upstream_gene_variant 0.13
Rv3236c 3613192 c.-76G>A upstream_gene_variant 0.4
fbiA 3640477 c.-66C>A upstream_gene_variant 0.22
alr 3840315 p.Gly369Asp missense_variant 0.2
rpoA 3878695 c.-188C>A upstream_gene_variant 0.18
ddn 3986760 c.-84G>A upstream_gene_variant 0.2
ddn 3986840 c.-4C>T upstream_gene_variant 0.4
clpC1 4040500 p.Gln69* stop_gained 0.22
panD 4043925 c.357C>T synonymous_variant 0.18
embA 4242292 c.-941C>T upstream_gene_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242969 p.Thr1036Ser missense_variant 0.17
embA 4243205 c.-28T>A upstream_gene_variant 0.33
embA 4244049 p.Asp273Asn missense_variant 0.22
embA 4244717 p.Trp495Cys missense_variant 0.12
embA 4244867 c.1635C>A synonymous_variant 0.15
embA 4246067 p.Asp945Glu missense_variant 0.2
embB 4249148 p.Ala879Thr missense_variant 0.33
embB 4249195 c.2682C>A synonymous_variant 0.29
embB 4249207 c.2694G>T synonymous_variant 0.29
aftB 4267116 p.Val574Ala missense_variant 0.29
aftB 4267353 p.Gly495Ala missense_variant 0.18
aftB 4267785 p.Gly351Glu missense_variant 1.0
aftB 4268088 p.Trp250* stop_gained 0.17
ubiA 4269589 p.Arg82Leu missense_variant 0.18
ubiA 4269854 c.-21G>A upstream_gene_variant 0.12
ethA 4326785 p.Pro230Leu missense_variant 0.29
ethR 4327594 p.Arg16Cys missense_variant 0.33
whiB6 4338201 c.321C>T synonymous_variant 0.17
whiB6 4338341 c.177_180dupGTGG frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0