TB-Profiler result

Run: SRR6046900
Summary

Run ID: SRR6046900

Sample name:

Date: 04-04-2023 12:25:09

Number of reads: 1142431

Percentage reads mapped: 75.17

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
gyrB 7175 p.Glu646Lys missense_variant 0.12
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 490749 c.-34G>A upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575394 p.Arg16Leu missense_variant 0.25
mshA 575575 c.228G>A synonymous_variant 0.17
ccsA 619835 c.-56G>T upstream_gene_variant 0.12
ccsA 620748 c.858T>G synonymous_variant 0.28
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761693 c.1887G>A synonymous_variant 0.15
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 763915 c.546C>T synonymous_variant 0.13
rpoC 764252 p.Arg295Trp missense_variant 0.12
rpoC 764643 c.1277delG frameshift_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766916 p.Arg1183Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 778167 p.Ala105Asp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781514 c.-46G>A upstream_gene_variant 0.2
fbiC 1305462 c.2532G>A synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473549 n.-109G>A upstream_gene_variant 0.2
rrl 1475432 n.1775G>T non_coding_transcript_exon_variant 1.0
rpsA 1833590 p.Gly17Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154607 p.Gln502Arg missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155534 p.Pro193Leu missense_variant 0.11
katG 2155703 p.Asp137Asn missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.26
eis 2715016 p.Arg106His missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.26
ahpC 2726636 c.444G>A synonymous_variant 0.12
folC 2746206 p.Gly465Arg missense_variant 0.12
pepQ 2860398 c.21A>C synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067377 p.Arg190Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449099 p.Ser199Tyr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474370 p.Ser122Gly missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612896 p.Gly74Asp missense_variant 0.14
fbiB 3642746 c.1212C>G synonymous_variant 0.12
rpoA 3878390 p.Arg40Ser missense_variant 0.13
clpC1 4038856 p.Lys617Glu missense_variant 0.11
clpC1 4040321 c.384C>T synonymous_variant 0.17
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 4242325 c.-908C>A upstream_gene_variant 0.12
embA 4242445 c.-788C>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244858 c.1626G>A synonymous_variant 0.17
embA 4244865 p.Ala545Ser missense_variant 0.17
embA 4244869 p.Ser546Asn missense_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247335 c.822C>T synonymous_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267595 c.1242C>T synonymous_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4270007 c.-174A>C upstream_gene_variant 0.14
ubiA 4270030 c.-197C>T upstream_gene_variant 0.22
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