TB-Profiler result

Run: SRR833035
Summary

Run ID: SRR833035

Sample name:

Date: 04-04-2023 20:57:37

Number of reads: 2860252

Percentage reads mapped: 84.73

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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 761109 p.Asp435Tyr missense_variant 0.98 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.39 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288868 p.Val125Asp missense_variant 1.0 pyrazinamide
folC 2747141 p.Glu153Ala missense_variant 0.98 para-aminosalicylic_acid
ald 3087136 c.317_318insT frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>T upstream_gene_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
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 490780 c.-3C>A upstream_gene_variant 0.2
ccsA 619951 p.Ala21Pro missense_variant 0.17
ccsA 619963 p.Leu25Val missense_variant 0.22
rpoB 761277 p.Ile491Leu missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.18
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.18
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.23
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.24
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.24
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.24
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.24
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.23
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.28
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.29
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.41
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.41
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.41
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.44
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.49
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.49
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.49
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.47
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.47
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.38
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.18
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.4
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.39
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.35
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.26
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.11
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.11
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.19
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.27
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.42
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.44
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.58
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715052 p.Arg94Leu missense_variant 0.2
thyX 3067419 p.Pro176Leu missense_variant 0.25
ald 3086772 c.-48A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642142 p.Asp203Ala missense_variant 0.12
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878559 c.-53_-52insC upstream_gene_variant 0.67
embC 4240559 p.Ala233Thr missense_variant 0.2
embC 4240563 p.Met234Thr missense_variant 0.2
embC 4240574 p.Val238Leu missense_variant 0.22
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243601 c.369C>T synonymous_variant 0.15
embB 4247882 p.Ala457Ser missense_variant 0.25
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407781 p.Ala141Glu missense_variant 0.99
gid 4407790 p.Ala138Val missense_variant 1.0