TB-Profiler result

Run: SRR11349137
Summary

Run ID: SRR11349137

Sample name:

Date: 02-04-2023 20:52:23

Number of reads: 5291238

Percentage reads mapped: 92.28

Strain: lineage4.4.1.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
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 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.3 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.3 linezolid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.91 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.98 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9158 c.1857C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.36
rpoC 765513 p.Lys715Thr 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 1472507 n.662C>G non_coding_transcript_exon_variant 0.18
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.15
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.15
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.15
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.15
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.15
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.2
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.2
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.39
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.39
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.38
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.42
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.43
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.43
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.43
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.45
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.47
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.45
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.45
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.45
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.45
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.45
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.39
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.39
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472816 n.971A>G non_coding_transcript_exon_variant 0.11
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.67
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.4
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.4
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.4
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.4
rrl 1474797 n.1140G>A non_coding_transcript_exon_variant 0.4
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.4
rrl 1474799 n.1142G>A non_coding_transcript_exon_variant 0.4
rrl 1474801 n.1144G>C non_coding_transcript_exon_variant 0.4
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.4
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.4
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.4
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.4
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.4
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.5
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.5
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.5
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.5
rrl 1474869 n.1212G>C non_coding_transcript_exon_variant 0.4
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.4
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.4
rrl 1475870 n.2213G>T non_coding_transcript_exon_variant 0.12
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.12
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.15
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.16
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.18
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.19
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.15
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.18
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.24
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.39
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 0.37
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.37
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.32
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155567 p.Gly182Glu missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726142 c.-51G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.39
fbiD 3339739 p.Ala208Thr missense_variant 0.12
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0