TB-Profiler result

Run: SRR5341222
Summary

Run ID: SRR5341222

Sample name:

Date: 04-04-2023 10:07:56

Number of reads: 541317

Percentage reads mapped: 81.74

Strain: lineage3.1

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
lineage3 East-African-Indian CAS RD750 0.97
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 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 6007 c.768C>T synonymous_variant 0.25
gyrA 6556 c.-746C>T upstream_gene_variant 0.14
gyrB 7087 p.Met616Ile missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 0.94
gyrA 7585 p.Ser95Thr missense_variant 0.92
gyrA 8564 c.1263G>T synonymous_variant 0.17
gyrA 8718 p.Glu473Lys missense_variant 0.15
gyrA 9177 p.Ala626Thr missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491139 p.Glu119Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620457 c.567C>A synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 0.91
rpoB 759914 c.108T>A synonymous_variant 0.14
rpoB 760207 c.410_412delACA disruptive_inframe_deletion 0.2
rpoB 760259 p.Phe151Leu missense_variant 0.22
rpoB 761457 p.Pro551Ser missense_variant 0.18
rpoB 761462 c.1656C>T synonymous_variant 0.18
rpoB 761465 c.1659G>T synonymous_variant 0.17
rpoB 761471 c.1665C>T synonymous_variant 0.18
rpoB 761477 c.1671C>G synonymous_variant 0.2
rpoB 761510 c.1704T>C synonymous_variant 0.29
rpoB 762255 p.Ala817Ser missense_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763124 c.-246C>A upstream_gene_variant 0.13
rpoC 763492 c.123G>T synonymous_variant 0.13
rpoC 763660 c.291T>G synonymous_variant 0.29
rpoC 763666 c.297G>T synonymous_variant 0.29
rpoC 763675 c.306C>G synonymous_variant 0.25
rpoC 763702 c.333C>G synonymous_variant 0.29
rpoC 763703 c.334_336delTCGinsAGC synonymous_variant 0.29
rpoC 763714 c.345G>C synonymous_variant 0.25
rpoC 763717 c.348T>C synonymous_variant 0.25
rpoC 763723 c.354G>C synonymous_variant 0.25
rpoC 763732 c.363C>G synonymous_variant 0.33
rpoC 763735 c.366G>C synonymous_variant 0.33
rpoC 763741 c.372C>T synonymous_variant 0.29
rpoC 763744 c.375G>C synonymous_variant 0.29
rpoC 763765 c.396T>C synonymous_variant 0.33
rpoC 764269 c.900G>T synonymous_variant 0.25
rpoC 764500 c.1131C>A synonymous_variant 0.25
rpoC 765336 p.Trp656Leu missense_variant 0.15
rpoC 765952 c.2583G>C synonymous_variant 0.2
rpoC 765967 c.2598C>T synonymous_variant 0.22
rpoC 765979 c.2610C>G synonymous_variant 0.25
rpoC 765982 c.2613C>G synonymous_variant 0.22
rpoC 765991 c.2622C>T synonymous_variant 0.22
rpoC 765994 c.2625A>T synonymous_variant 0.22
rpoC 766010 c.2641_2642delTCinsAG synonymous_variant 0.18
rpoC 766021 c.2652G>C synonymous_variant 0.2
rpoC 766027 c.2658G>C synonymous_variant 0.25
rpoC 766043 p.Gln892Glu missense_variant 0.2
rpoC 766061 p.Val898Ile missense_variant 0.15
rpoC 766441 c.3072C>A synonymous_variant 0.18
rpoC 767157 p.Gly1263Val missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776906 c.1575G>A synonymous_variant 0.2
mmpL5 777761 c.720G>T synonymous_variant 0.25
mmpL5 778282 p.Asp67His missense_variant 0.4
mmpR5 779254 p.Arg89Trp missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781468 c.-91delC upstream_gene_variant 0.33
rpsL 781868 c.309T>C synonymous_variant 0.13
rpsL 781871 c.312G>C synonymous_variant 0.12
rplC 800831 p.Gly8Asp missense_variant 0.18
rplC 801195 c.387G>T synonymous_variant 0.33
Rv1258c 1406893 p.Leu150Ile missense_variant 0.14
embR 1416435 c.912delA frameshift_variant 0.5
embR 1416782 p.Ala189Glu missense_variant 0.17
embR 1416795 p.Gly185Trp missense_variant 0.13
atpE 1461113 c.69C>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>A non_coding_transcript_exon_variant 0.15
rrs 1472790 n.945T>A non_coding_transcript_exon_variant 0.18
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.11
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.11
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.12
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.12
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.13
inhA 1673466 c.-736C>A upstream_gene_variant 0.29
rpsA 1833880 p.Trp113Cys missense_variant 0.2
tlyA 1917893 c.-47G>A upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101731 p.Ala438Ser missense_variant 0.22
ndh 2102359 c.684C>T synonymous_variant 0.22
ndh 2103225 c.-183A>C upstream_gene_variant 0.25
katG 2154445 p.Ala556Glu missense_variant 0.14
katG 2154557 p.Arg519Ser missense_variant 0.18
katG 2154724 p.Arg463Met missense_variant 1.0
katG 2154887 p.Ala409Ser missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168816 c.1796delG frameshift_variant 0.18
PPE35 2169435 p.Asn393Ser missense_variant 0.25
PPE35 2169850 p.Asn255Asp missense_variant 0.13
Rv1979c 2223103 p.Met21Lys missense_variant 0.17
Rv1979c 2223192 c.-28G>T upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288884 c.358C>T synonymous_variant 0.2
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289320 c.-81_-80delCG upstream_gene_variant 0.17
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289514 c.-273C>T upstream_gene_variant 0.17
kasA 2517980 c.-135C>T upstream_gene_variant 0.15
eis 2714559 c.774C>G synonymous_variant 0.33
ahpC 2726105 c.-88G>A upstream_gene_variant 0.93
ahpC 2726343 p.Phe51Val missense_variant 0.29
pepQ 2859582 c.837G>A synonymous_variant 0.25
pepQ 2859902 p.Ser173Gly missense_variant 0.15
Rv2752c 3066182 p.Asp4Asn missense_variant 0.33
Rv2752c 3066998 c.-807G>A upstream_gene_variant 0.15
thyX 3067793 c.153T>C synonymous_variant 0.2
thyX 3067799 c.147G>A synonymous_variant 0.18
thyX 3067802 c.144C>G synonymous_variant 0.18
thyX 3067814 c.132T>C synonymous_variant 0.18
thyX 3067823 c.123G>C synonymous_variant 0.18
thyX 3067826 c.120C>G synonymous_variant 0.18
thyX 3067847 c.99C>G synonymous_variant 0.18
thyX 3067850 c.96A>C synonymous_variant 0.2
thyX 3067874 c.72C>G synonymous_variant 0.17
thyX 3067883 c.63C>G synonymous_variant 0.15
thyX 3067889 c.57C>A synonymous_variant 0.17
thyX 3067898 p.Asp16Glu missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339108 c.-10G>T upstream_gene_variant 0.15
Rv3083 3449760 c.1257G>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.9
fprA 3474425 p.Gln140Pro missense_variant 1.0
Rv3236c 3612085 c.1032C>T synonymous_variant 0.29
Rv3236c 3612755 p.Leu121Arg missense_variant 0.33
Rv3236c 3613001 c.115delG frameshift_variant 0.18
fbiB 3641639 c.105G>A synonymous_variant 0.2
fbiB 3642482 p.Lys316Asn missense_variant 0.18
alr 3840211 p.Glu404Lys missense_variant 0.14
alr 3840766 p.Leu219Met missense_variant 0.18
alr 3841037 c.384G>T synonymous_variant 0.25
clpC1 4039107 p.Arg533Leu missense_variant 0.14
clpC1 4039796 c.909C>T synonymous_variant 0.15
clpC1 4039824 p.Gly294Val missense_variant 0.14
embC 4239973 c.111T>G synonymous_variant 0.29
embC 4240098 p.Ala79Asp missense_variant 0.18
embC 4240285 c.423C>A synonymous_variant 0.29
embC 4240623 p.Ala254Asp missense_variant 0.29
embC 4242058 c.2196G>A synonymous_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.8
embB 4247218 c.705G>T synonymous_variant 0.13
embB 4247399 p.Asn296Tyr missense_variant 0.15
embB 4247947 p.Leu478Phe missense_variant 0.29
embB 4248021 c.1510delG frameshift_variant 0.18
embB 4249334 p.Ala941Thr missense_variant 0.22
embB 4249574 p.Lys1021* stop_gained 0.17
aftB 4267296 p.Leu514* stop_gained 0.29
aftB 4267387 p.His484Asn missense_variant 0.18
ethA 4327308 p.Asp56Tyr missense_variant 0.33
ethA 4327623 c.-150A>T upstream_gene_variant 0.25
ethR 4327813 p.Thr89Pro missense_variant 0.4
ethA 4327827 c.-354A>G upstream_gene_variant 0.5
whiB6 4338471 p.Arg17Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408343 c.-141C>A upstream_gene_variant 0.2