TB-Profiler result

Run: SRR12199486
Summary

Run ID: SRR12199486

Sample name:

Date: 03-04-2023 06:43:28

Number of reads: 622263

Percentage reads mapped: 36.3

Strain: lineage2.2.1

Drug-resistance: Other

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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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.12 streptomycin
ethA 4326438 c.1032_1035dupGAAC frameshift_variant 0.12 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576786 p.Ala480Val missense_variant 0.2
ccsA 620526 c.636G>A synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763501 p.Asp44Glu missense_variant 1.0
rpoC 764856 c.1488delG frameshift_variant 0.14
rpoC 765496 c.2127C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777353 c.1128G>T synonymous_variant 0.17
mmpL5 778400 p.Met27Ile missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304216 p.Asn429Ser missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461199 p.Pro52Gln missense_variant 0.12
atpE 1461226 p.Glu61Gly missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.11
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.11
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.12
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.13
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.1
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.14
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.11
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.22
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.16
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.12
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.11
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.11
rrl 1474564 n.907G>A non_coding_transcript_exon_variant 0.22
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.11
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.11
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.1
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.13
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.13
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.19
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.14
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.14
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.21
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.21
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.32
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.28
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.1
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
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 2167955 c.2658A>C synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288716 p.Arg176Cys missense_variant 0.17
ribD 2987027 c.189C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642282 p.Glu250Lys missense_variant 0.15
fbiB 3642389 c.855C>A synonymous_variant 0.12
fbiB 3642692 c.1158C>A synonymous_variant 0.14
clpC1 4038162 p.Arg848Leu missense_variant 0.15
clpC1 4039240 p.Gly489Cys missense_variant 0.14
clpC1 4039252 p.Ala485Ser missense_variant 0.14
clpC1 4039283 c.1422C>T synonymous_variant 0.14
clpC1 4039305 p.Gln467Arg missense_variant 0.15
clpC1 4039695 p.Ala337Glu missense_variant 0.14
embC 4241677 c.1815G>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.1
embA 4244448 c.1220delC frameshift_variant 0.1
embA 4244877 p.Ala549Thr missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
aftB 4267644 p.Asp398Gly missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267968 p.Leu290Pro missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407981 c.222G>A synonymous_variant 0.12