TB-Profiler result

Run: SRR11972215
Summary

Run ID: SRR11972215

Sample name:

Date: 03-04-2023 05:32:16

Number of reads: 205427

Percentage reads mapped: 98.38

Strain: lineage4.5

Drug-resistance: RR-TB

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.5 Euro-American H;T RD122 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
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.25 kanamycin, capreomycin, aminoglycosides, amikacin
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 5465 p.Glu76Gln missense_variant 0.12
gyrB 7113 p.Thr625Ile missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
fgd1 490729 c.-54C>T upstream_gene_variant 0.4
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 761867 c.2061C>T synonymous_variant 0.15
rpoB 762324 p.Lys840Glu missense_variant 0.25
rpoB 762507 p.Leu901Ile missense_variant 0.22
rpoC 763829 p.Glu154Lys missense_variant 0.2
rpoC 765346 c.1977C>A synonymous_variant 0.22
rpoC 765403 c.2034G>A synonymous_variant 0.29
rpoC 766023 p.Ile885Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775935 p.Asp849Val missense_variant 0.22
mmpL5 777747 p.Gly245Glu missense_variant 0.29
mmpR5 778385 c.-605C>T upstream_gene_variant 0.25
mmpL5 778651 c.-171C>T upstream_gene_variant 0.2
mmpL5 778917 c.-437A>C upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781756 p.Tyr66Phe missense_variant 0.15
fbiC 1304975 p.Lys682Met missense_variant 0.12
Rv1258c 1407380 c.-40C>T upstream_gene_variant 1.0
embR 1416751 p.Phe199Leu missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474303 n.646A>T non_coding_transcript_exon_variant 1.0
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.17
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.18
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.18
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.18
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.18
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.18
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.15
rrl 1474674 n.1017A>C non_coding_transcript_exon_variant 0.15
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.15
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.15
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.15
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.14
rrl 1474821 n.1164T>C non_coding_transcript_exon_variant 0.15
rrl 1475194 n.1538dupG non_coding_transcript_exon_variant 0.4
rrl 1475453 n.1796T>A non_coding_transcript_exon_variant 0.17
rrl 1475482 n.1825A>T non_coding_transcript_exon_variant 0.13
rpsA 1834298 p.Gln253Glu missense_variant 0.22
tlyA 1918304 p.Leu122Pro missense_variant 0.4
tlyA 1918345 p.Ala136Ser missense_variant 0.25
katG 2154295 p.Ala606Val missense_variant 0.12
katG 2156344 c.-233C>T upstream_gene_variant 0.33
katG 2156355 c.-244C>T upstream_gene_variant 0.33
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167814 c.2799C>T synonymous_variant 0.22
PPE35 2167825 c.2780_2787delTGCTAGCC frameshift_variant 0.21
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.27
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518607 p.Met165Val missense_variant 0.17
Rv2752c 3065227 p.Glu322Gly missense_variant 0.23
thyX 3067643 p.Tyr101* stop_gained 0.18
thyX 3067921 p.Val9Met missense_variant 0.2
ald 3086689 c.-131G>T upstream_gene_variant 0.13
ald 3086776 c.-44G>A upstream_gene_variant 0.15
ald 3087655 p.Arg279Leu missense_variant 0.33
fbiD 3339480 p.Gln121His missense_variant 1.0
Rv3083 3449065 p.Thr188Ala missense_variant 0.4
fprA 3473815 c.-192G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612618 p.Pro167Ser missense_variant 0.67
alr 3840570 p.Val284Ala missense_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.14
rpoA 3878455 c.52dupC frameshift_variant 0.12
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
ddn 3986744 c.-100C>T upstream_gene_variant 0.13
ddn 3987072 p.Ala77Ser missense_variant 0.29
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243482 p.Ala84Ser missense_variant 1.0
embA 4243507 p.Thr92Ile missense_variant 0.25
embA 4243673 c.441C>T synonymous_variant 0.25
embA 4245853 p.Ala874Val missense_variant 0.33
embB 4248206 p.Ser565Arg missense_variant 1.0
aftB 4266958 p.Glu627Lys missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0