TB-Profiler result

Run: ERR270771
Summary

Run ID: ERR270771

Sample name:

Date: 31-03-2023 23:26:44

Number of reads: 2517102

Percentage reads mapped: 75.37

Strain: lineage3

Drug-resistance: HR-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 0.98
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.77 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.22 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 8948 c.1647G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491414 p.Val211Ala missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472147 n.302G>T non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.16
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.27
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.25
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.25
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.24
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.24
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.26
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.24
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.2
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.15
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.16
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.31
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472573 n.728C>G non_coding_transcript_exon_variant 0.34
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.33
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.29
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.28
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.28
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.23
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.14
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.16
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.15
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.15
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.17
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.17
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.16
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.11
rrl 1474824 n.1167A>C non_coding_transcript_exon_variant 0.11
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.21
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.35
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.35
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.42
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.35
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.11
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.96
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ahpC 2726338 p.Val49Gly missense_variant 0.37
thyA 3073806 c.666C>G synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840354 p.Asp356Gly missense_variant 0.95
clpC1 4038857 c.1848C>A synonymous_variant 0.3
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407703 p.Ala167Asp missense_variant 0.92