TB-Profiler result

Run: SRR11972163
Summary

Run ID: SRR11972163

Sample name:

Date: 03-04-2023 05:30:33

Number of reads: 452612

Percentage reads mapped: 98.78

Strain: lineage1

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
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 7637 c.336C>A synonymous_variant 0.17
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8647 p.Gln449Arg missense_variant 0.2
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
gyrA 9791 c.2490C>A synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575150 c.-198C>T upstream_gene_variant 0.29
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 759832 p.Thr9Lys missense_variant 0.15
rpoB 759939 p.Pro45Thr missense_variant 0.17
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763286 c.-84G>T upstream_gene_variant 0.17
rpoC 763849 c.480G>A synonymous_variant 0.18
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766233 p.Ala955Asp missense_variant 0.33
rpoC 766786 p.Gln1139His missense_variant 0.25
rpoC 767206 c.3837C>T synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.92
mmpL5 777560 c.921C>A synonymous_variant 0.4
mmpL5 777907 p.Leu192Met missense_variant 0.5
mmpR5 778088 c.-902C>G upstream_gene_variant 1.0
mmpR5 778094 c.-896A>G upstream_gene_variant 1.0
mmpL5 778386 p.Ala32Val missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800922 c.114C>A synonymous_variant 0.13
fbiC 1302898 c.-33G>T upstream_gene_variant 0.22
fbiC 1303434 p.Asp168Glu missense_variant 0.17
fbiC 1305187 p.Leu753Met missense_variant 0.25
embR 1416232 p.Cys372Gly missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472193 n.348A>T non_coding_transcript_exon_variant 0.14
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.29
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.17
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.14
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.14
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.12
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.18
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.18
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.19
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.17
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.13
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
rpsA 1833855 p.Lys105Arg missense_variant 0.2
rpsA 1834720 c.1179C>A synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102396 p.Ala216Val missense_variant 0.22
ndh 2102653 p.His130Glu missense_variant 0.15
ndh 2102875 c.168C>T synonymous_variant 0.18
katG 2154240 p.Met624Ile missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168946 p.Pro556Leu missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.13
PPE35 2170357 p.Ala86Thr missense_variant 0.18
PPE35 2170518 p.Asp32Ala missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288821 p.Gln141Lys missense_variant 0.2
pncA 2289272 c.-31C>T upstream_gene_variant 0.67
pncA 2290179 c.-938G>T upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519159 p.Ala349Ser missense_variant 0.2
eis 2714742 p.Trp197Cys missense_variant 0.15
eis 2714827 p.Thr169Asn missense_variant 0.25
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.24
ahpC 2726631 p.Val147Phe missense_variant 0.14
folC 2747427 p.Gly58Ser missense_variant 0.4
folC 2747551 c.48C>A synonymous_variant 0.2
pepQ 2860485 c.-67C>A upstream_gene_variant 0.12
ribD 2986760 c.-79C>A upstream_gene_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065032 p.Gly387Val missense_variant 0.22
Rv2752c 3065089 p.Ala368Glu missense_variant 0.2
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
Rv2752c 3065847 p.Lys115Asn missense_variant 0.22
Rv2752c 3066080 p.Gly38Cys missense_variant 0.13
thyA 3074653 c.-182G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449301 c.798G>T synonymous_variant 0.22
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 3613197 c.-81G>A upstream_gene_variant 0.2
fbiA 3640832 p.Val97Ala missense_variant 0.2
rpoA 3878578 c.-71C>A upstream_gene_variant 0.29
ddn 3987057 p.Arg72Trp missense_variant 1.0
clpC1 4039654 p.Thr351Ser missense_variant 0.18
clpC1 4040335 p.Leu124Val missense_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240288 c.426C>A synonymous_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242099 p.Gly746Asp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244305 p.Arg358Leu missense_variant 0.25
embB 4245671 c.-843C>A upstream_gene_variant 0.22
embA 4245882 p.Gly884Cys missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246236 p.Leu1002Ile missense_variant 0.33
embB 4246723 c.210G>T synonymous_variant 1.0
embB 4247546 p.Asp345Tyr missense_variant 0.4
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249329 p.Met939Arg missense_variant 0.2
embB 4249395 p.Ile961Thr missense_variant 0.12
aftB 4267250 p.Asp529Glu missense_variant 0.15
aftB 4267430 c.1407G>T synonymous_variant 0.2
aftB 4267953 p.Ala295Val missense_variant 0.33
aftB 4268424 p.Gly138Val missense_variant 0.17
ubiA 4269325 p.Ile170Thr missense_variant 0.12
ubiA 4269346 p.Ala163Val missense_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269467 p.Asn123His missense_variant 0.25
aftB 4269471 c.-635C>G upstream_gene_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 0.83
aftB 4269636 c.-800C>A upstream_gene_variant 0.4
ethA 4326482 p.Arg331Leu missense_variant 0.33
ethR 4327051 c.-498G>A upstream_gene_variant 0.29
whiB6 4338384 p.Asp46Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338617 c.-96C>A upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0