TB-Profiler result

Run: SRR6797359

Summary

Run ID: SRR6797359

Sample name:

Date: 04-04-2023 16:07:15

Number of reads: 974644

Percentage reads mapped: 97.73

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_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 760353 p.Glu183* stop_gained 0.25
rpoB 761769 p.Met655Val missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763675 c.306C>A synonymous_variant 0.12
rpoC 763884 p.Ala172Val missense_variant 0.9
rpoC 763886 c.517C>A synonymous_variant 0.89
rpoC 764748 p.Leu460Pro missense_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779248 p.Gly87Arg missense_variant 1.0
mmpL5 779370 c.-890G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406503 p.Val280Leu missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 1.0
rrl 1475320 n.1663T>G non_coding_transcript_exon_variant 0.13
rrl 1475950 n.2293C>T non_coding_transcript_exon_variant 0.12
rpsA 1834493 p.Glu318* stop_gained 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.92
PPE35 2168136 p.Ile826Thr missense_variant 0.1
PPE35 2170066 p.Ala183Thr missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222916 c.249G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289243 c.-3_-2insC upstream_gene_variant 1.0
pncA 2290064 c.-823C>T upstream_gene_variant 0.11
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715148 p.Ala62Val missense_variant 0.11
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726335 p.Arg48Gln missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087243 p.Ala142Thr missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449188 p.Val229Ile 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 3611987 p.Leu377Pro missense_variant 0.1
rpoA 3877844 p.Ala222Ser missense_variant 0.25
rpoA 3877932 c.576G>T synonymous_variant 0.18
clpC1 4038215 c.2490G>A synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
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 4243848 p.Val206Met missense_variant 1.0
embA 4245934 p.Pro901Leu missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248570 p.Leu686Pro missense_variant 0.14
aftB 4267794 p.Ala348Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.97
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