TB-Profiler result

Run: SRR18213723
Summary

Run ID: SRR18213723

Sample name:

Date: 03-04-2023 19:26:30

Number of reads: 402235

Percentage reads mapped: 95.43

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 5598 p.Leu120Arg missense_variant 0.13
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 7802 c.501C>A synonymous_variant 0.2
gyrA 8352 p.Gly351Arg missense_variant 0.14
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8708 c.1407G>A synonymous_variant 0.25
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9798 p.Ala833Thr missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575871 p.His175Leu missense_variant 0.29
ccsA 620378 p.Val163Ala missense_variant 0.25
ccsA 620457 c.567C>A synonymous_variant 0.14
ccsA 620532 c.642T>G synonymous_variant 0.17
ccsA 620748 c.858T>G synonymous_variant 0.36
rpoB 762005 p.Asn733Lys missense_variant 0.18
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 764927 p.Lys520Glu missense_variant 0.1
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765988 c.2619G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775716 p.Arg922Gln missense_variant 0.17
mmpL5 775864 p.Ala873Thr missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778046 c.-944C>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801211 p.Gln135* stop_gained 0.22
Rv1258c 1406553 p.Ala263Val missense_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 1.0
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 1.0
fabG1 1673560 p.Lys41* stop_gained 0.22
rpsA 1833732 p.Pro64His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154294 c.1818C>T synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154784 p.Pro443Leu missense_variant 0.13
katG 2155383 c.729C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169639 p.Gly325Asp missense_variant 0.25
Rv1979c 2222244 c.921A>G synonymous_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289599 c.-358A>G upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715266 p.Ser23Gly missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94
ahpC 2726269 p.Val26Gly missense_variant 0.2
ahpC 2726468 c.276G>A synonymous_variant 1.0
folC 2747102 p.Ala166Glu missense_variant 0.13
pepQ 2859398 p.Thr341Ala missense_variant 0.12
ribD 2986645 c.-194G>A upstream_gene_variant 1.0
ribD 2987036 c.198C>T synonymous_variant 0.2
ribD 2987534 c.696G>T synonymous_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065635 p.Pro186Leu missense_variant 0.25
Rv2752c 3065951 p.His81Tyr missense_variant 1.0
thyX 3067491 p.Ala152Val missense_variant 1.0
thyA 3074652 c.-181T>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086928 p.Ala37Pro missense_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475004 p.Pro333Leu missense_variant 0.4
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613247 c.-131C>T upstream_gene_variant 0.17
fbiA 3640446 c.-97A>T upstream_gene_variant 1.0
clpC1 4040126 c.579C>A synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240648 c.786C>T synonymous_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240897 c.1035C>A synonymous_variant 0.18
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241675 p.Ala605Thr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243582 p.Ala117Val missense_variant 0.22
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245234 p.Met668Leu missense_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247482 c.969C>T synonymous_variant 0.14
embB 4247490 p.Pro326Leu missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249030 c.2518delG frameshift_variant 0.17
aftB 4267136 p.Gln567His missense_variant 0.2
aftB 4268354 c.483G>A synonymous_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326178 p.Met432Ile missense_variant 0.13
ethA 4326202 c.1272A>G synonymous_variant 0.11
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