TB-Profiler result

Run: ERR3077963
Summary

Run ID: ERR3077963

Sample name:

Date: 01-04-2023 00:12:59

Number of reads: 1948471

Percentage reads mapped: 94.97

Strain: lineage4.2.2.2;lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 0.58
lineage4 Euro-American LAM;T;S;X;H None 0.37
lineage4.2 Euro-American H;T;LAM None 0.39
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.53
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.39
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.59
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.37
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 761100 p.Gln432Glu missense_variant 0.36 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.64 rifampicin
rpsL 781822 p.Lys88Met missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288859 p.Val128Gly missense_variant 0.57 pyrazinamide
embB 4247513 p.Tyr334His missense_variant 0.26 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.76 ethambutol
ethA 4326208 c.1265_1266insT frameshift_variant 0.76 ethionamide
gid 4407731 c.471delG frameshift_variant 0.45 streptomycin
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 8688 p.Ala463Ser missense_variant 0.46
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.65
mshA 576077 c.730C>T synonymous_variant 0.42
ccsA 619831 c.-60T>G upstream_gene_variant 0.24
ccsA 619836 c.-55A>T upstream_gene_variant 0.11
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
rpoB 759746 c.-61C>T upstream_gene_variant 0.5
rpoB 761248 p.Glu481Ala missense_variant 0.39
rpoB 761407 p.Val534Ala missense_variant 0.64
rpoB 761489 c.1683G>A synonymous_variant 0.38
rpoC 762434 c.-936T>G upstream_gene_variant 0.68
rpoC 763031 c.-339T>C upstream_gene_variant 0.64
rpoC 766740 p.Val1124Gly missense_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.55
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.12
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.11
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.19
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.23
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.21
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.11
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.11
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.11
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.11
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.11
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.11
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.23
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.35
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.37
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.32
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.3
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.32
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.31
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.12
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.13
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.13
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.13
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.13
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.13
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.13
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.13
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.13
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.76
PPE35 2167926 p.Leu896Ser missense_variant 0.62
PPE35 2170461 p.Gly51Glu missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288911 p.Glu111* stop_gained 0.33
pncA 2289047 c.195C>T synonymous_variant 0.6
pncA 2289365 c.-125delC upstream_gene_variant 0.59
ahpC 2726105 c.-88G>A upstream_gene_variant 0.59
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.42
ald 3086742 c.-78A>C upstream_gene_variant 0.37
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240172 p.Val104Met missense_variant 0.58
embC 4241562 p.Arg567His missense_variant 0.75
embC 4242075 p.Arg738Gln missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243323 p.Val31Ile missense_variant 0.71
ethR 4328051 p.Ala168Val missense_variant 0.53
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.36