TB-Profiler result

Run: SRR1172753

Summary

Run ID: SRR1172753

Sample name:

Date: 03-04-2023 03:09:50

Number of reads: 1501413

Percentage reads mapped: 27.05

Strain: lineage4.4.1.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 0.98
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans None 0.99
lineage4.4.1.1.1 Euro-American S;Orphans None 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
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.83 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 5861 p.Leu208Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575891 p.Ala182Ser missense_variant 0.15
mshA 576488 p.Val381His missense_variant 0.15
ccsA 620172 c.282C>T synonymous_variant 0.18
rpoB 762846 p.Pro1014Thr missense_variant 0.15
rpoC 763840 c.471G>T synonymous_variant 0.12
rpoC 764332 c.963G>T synonymous_variant 0.14
rpoC 765473 p.Glu702Lys missense_variant 0.13
rpoC 766003 c.2634G>T synonymous_variant 0.12
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775592 p.Leu963Phe missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777422 c.1059G>T synonymous_variant 0.22
mmpL5 778091 p.Trp130Cys missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303867 p.Asp313Tyr missense_variant 0.15
fbiC 1303880 p.Thr317Met missense_variant 0.15
fbiC 1304311 p.Ala461Ser missense_variant 0.13
Rv1258c 1407446 c.-106G>A upstream_gene_variant 0.16
embR 1417011 p.Gly113Trp missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472120 n.275G>T non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.6
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.71
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.7
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.81
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.81
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.83
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.83
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.9
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.9
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.9
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.9
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.9
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.87
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.36
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.76
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.77
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.85
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.85
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.83
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.82
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.77
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.38
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.13
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.13
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.13
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.12
rrl 1475246 n.1589C>A non_coding_transcript_exon_variant 0.17
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.33
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.32
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.31
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.3
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.3
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.21
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.19
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.62
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.65
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.74
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.77
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.8
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.81
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.54
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.36
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.18
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rpsA 1833403 c.-139G>T upstream_gene_variant 0.14
tlyA 1917857 c.-83C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918643 p.Gly235Val missense_variant 0.2
ndh 2102263 p.Lys260Asn missense_variant 0.13
ndh 2102889 p.Gln52Lys missense_variant 0.22
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154850 p.Gly421Asp missense_variant 0.12
katG 2155745 p.Gly123Arg missense_variant 0.17
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170409 c.204G>T synonymous_variant 0.14
PPE35 2170438 p.Gly59Arg missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289813 c.-572G>T upstream_gene_variant 0.14
pncA 2290108 c.-867C>A upstream_gene_variant 0.12
pncA 2290203 c.-962C>T upstream_gene_variant 0.12
kasA 2518529 p.Pro139Thr missense_variant 0.12
kasA 2518759 c.645C>A synonymous_variant 0.22
eis 2714512 p.Pro274Gln missense_variant 0.13
eis 2715045 c.288G>A synonymous_variant 0.13
folC 2746576 c.1023C>T synonymous_variant 0.15
pepQ 2859606 c.813G>T synonymous_variant 0.12
pepQ 2859922 p.Gly166Val missense_variant 0.15
pepQ 2859979 p.Cys147Tyr missense_variant 0.2
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2987040 c.202C>A synonymous_variant 0.17
Rv2752c 3064565 p.Glu543Lys missense_variant 0.15
Rv2752c 3064993 p.Trp400* stop_gained 0.96
thyX 3067374 p.Ala191Asp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474228 c.222C>A synonymous_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642287 c.753G>T synonymous_variant 0.12
rpoA 3877580 p.Asp310His missense_variant 0.12
clpC1 4038444 p.Ala754Glu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242891 p.Arg1010Leu missense_variant 0.21
embC 4243026 p.Arg1055Met missense_variant 0.17
embA 4243719 p.Pro163Ser missense_variant 0.15
embA 4244472 p.Val414Leu missense_variant 0.13
embA 4244686 p.Ile485Thr missense_variant 0.11
embA 4245723 p.Gly831Arg missense_variant 0.14
aftB 4267526 c.1311C>A synonymous_variant 0.15
aftB 4268599 p.Glu80* stop_gained 0.13
ubiA 4269671 p.Val55Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0