TB-Profiler result

Run: SRR11972222
Summary

Run ID: SRR11972222

Sample name:

Date: 03-04-2023 05:32:29

Number of reads: 551933

Percentage reads mapped: 99.3

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 0.99
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 6159 p.Thr307Ile missense_variant 0.12
gyrA 6334 c.-968G>A upstream_gene_variant 0.33
gyrB 6417 p.Thr393Ile missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7993 p.Ala231Asp missense_variant 0.12
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8952 p.Gln551Lys missense_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9278 c.1977G>A synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620094 c.204G>A synonymous_variant 0.14
rpoB 759841 p.Ser12Asn missense_variant 0.12
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 762542 c.-828C>T upstream_gene_variant 1.0
rpoB 762768 p.Pro988Ser missense_variant 0.15
rpoB 763017 p.Gln1071* stop_gained 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763403 p.Ile12Val missense_variant 0.11
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764081 c.716delA frameshift_variant 0.18
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766942 c.3573C>T synonymous_variant 0.25
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 776488 p.Gln665* stop_gained 0.22
mmpL5 776780 p.Leu567Phe missense_variant 0.14
mmpL5 777342 p.Arg380Tyr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800680 c.-129T>C upstream_gene_variant 0.13
rplC 801273 c.465C>T synonymous_variant 0.12
rplC 801313 p.Arg169Trp missense_variant 0.12
fbiC 1302903 c.-28T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474828 n.1171G>A non_coding_transcript_exon_variant 0.12
fabG1 1673224 c.-215_-199delATACCTGCTGCGCAATT upstream_gene_variant 1.0
tlyA 1917877 c.-63T>C upstream_gene_variant 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 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222459 p.Glu236* stop_gained 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288975 c.267A>T synonymous_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518276 p.Trp54Cys missense_variant 1.0
eis 2715535 c.-203T>A upstream_gene_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746146 p.Asp485His missense_variant 1.0
folC 2747494 c.105C>T synonymous_variant 0.18
folC 2747559 p.Ala14Thr missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064916 p.Gly426Cys missense_variant 0.12
Rv2752c 3064945 p.Pro416Arg missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087347 c.528C>T synonymous_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449302 p.Arg267* stop_gained 0.2
Rv3083 3449798 p.Asp432Gly missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474868 p.Val288Met missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3613057 c.60G>A synonymous_variant 0.18
Rv3236c 3613080 p.Val13Phe missense_variant 0.17
fbiA 3641156 p.Asp205Gly missense_variant 0.12
clpC1 4040021 c.684A>C synonymous_variant 0.12
clpC1 4040024 c.681A>G synonymous_variant 0.13
clpC1 4040027 c.678C>G synonymous_variant 0.13
clpC1 4040032 p.Val225Ile missense_variant 0.13
clpC1 4040057 c.648C>T synonymous_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040732 c.-28G>C upstream_gene_variant 0.12
embC 4239862 c.-1G>A upstream_gene_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 4242880 c.-353A>T upstream_gene_variant 0.12
embA 4243848 p.Val206Met missense_variant 1.0
embB 4245899 c.-615C>T upstream_gene_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246833 p.Lys107Met missense_variant 0.25
embB 4247271 p.Leu253Pro missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267234 p.Asp535Asn missense_variant 0.12
aftB 4267252 p.Asp529Asn missense_variant 0.12
aftB 4268045 p.Tyr264* stop_gained 0.15
aftB 4268065 p.Ser258Pro missense_variant 0.17
aftB 4268655 p.Thr61Ile missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269708 c.-872C>T upstream_gene_variant 0.13
ethA 4327071 p.Phe135Leu missense_variant 0.14
ethA 4327206 p.Ala90Thr missense_variant 0.2
ethA 4327421 p.Ser18Asn missense_variant 0.15
ethA 4328291 c.-818C>G upstream_gene_variant 0.2
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 4407871 p.Ala111Val missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408082 p.Val41Ile missense_variant 0.12