TB-Profiler result

Run: ERR036211
Summary

Run ID: ERR036211

Sample name:

Date: 31-03-2023 08:29:55

Number of reads: 1168771

Percentage reads mapped: 93.55

Strain: lineage4.9;lineage4.3.4.2.1;lineage1.1.3.2

Drug-resistance: Other

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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 0.69
lineage1 Indo-Oceanic EAI RD239 0.19
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.06
lineage4.9 Euro-American (H37Rv-like) T1 None 0.09
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.14
lineage4.3.4 Euro-American (LAM) LAM RD174 0.56
lineage1.1.3.2 Indo-Oceanic NA RD239 0.07
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.42
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.51
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.16 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
gyrB 6112 p.Met291Ile missense_variant 0.31
gyrB 6140 p.Val301Leu missense_variant 0.3
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.92
gyrA 8188 p.Leu296Pro missense_variant 0.16
gyrA 8445 p.Arg382Gly missense_variant 0.29
gyrA 9143 c.1842T>C synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 0.95
fgd1 491742 c.960T>C synonymous_variant 0.35
ccsA 619695 c.-196G>A upstream_gene_variant 0.15
ccsA 620659 p.Arg257Cys missense_variant 0.16
rpoB 759831 p.Thr9Pro missense_variant 0.25
rpoB 762249 p.Leu815Val missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 0.19
rpoC 763886 c.517C>A synonymous_variant 0.18
rpoC 764725 p.Phe452Leu missense_variant 0.26
rpoC 764995 c.1626C>G synonymous_variant 0.59
rpoC 765171 p.Pro601Leu missense_variant 0.19
rpoC 765230 p.Ala621Thr missense_variant 0.32
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.35
mmpL5 778078 p.Thr135Ala missense_variant 0.28
mmpS5 778605 p.Pro101Ala missense_variant 0.14
mmpR5 779371 p.Ala128Pro missense_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.26
rplC 801166 p.Gly120Ser missense_variant 0.17
fbiC 1303629 p.Ser233Arg missense_variant 0.27
fbiC 1303964 p.Ala345Gly missense_variant 0.19
embR 1417019 p.Cys110Tyr missense_variant 0.15
atpE 1461019 c.-26C>A upstream_gene_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.12
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.14
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.17
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.12
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.12
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.12
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.13
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.23
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.2
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.11
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.27
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.28
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.28
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.28
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.45
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.35
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 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
rpsA 1833712 p.Tyr57* stop_gained 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.42
PPE35 2167926 p.Leu896Ser missense_variant 0.38
PPE35 2167983 p.Gly877Asp missense_variant 0.15
PPE35 2169866 c.747G>C synonymous_variant 0.5
PPE35 2170090 p.Pro175Ser missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 0.2
eis 2714366 p.Val323Leu missense_variant 0.18
eis 2715586 c.-254G>C upstream_gene_variant 0.33
ahpC 2725954 c.-239C>T upstream_gene_variant 0.3
ahpC 2726051 c.-142G>A upstream_gene_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 0.19
ahpC 2726756 c.564C>G synonymous_variant 0.33
pepQ 2859748 p.Ala224Val missense_variant 0.11
ribD 2987307 p.Ala157Pro missense_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.32
Rv2752c 3067191 c.-1000G>A upstream_gene_variant 0.15
thyA 3073817 p.Gln219Glu missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 0.92
fbiD 3339153 p.Leu12Phe missense_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
fprA 3475159 p.Asn385Asp missense_variant 0.18
Rv3236c 3612009 p.Ala370Thr missense_variant 0.4
fbiB 3642734 c.1200G>C synonymous_variant 0.6
alr 3840719 c.702A>G synonymous_variant 0.33
rpoA 3878687 c.-180A>C upstream_gene_variant 0.23
ddn 3987013 p.Gly57Ala missense_variant 0.32
clpC1 4038287 c.2418C>T synonymous_variant 0.5
clpC1 4039932 p.Gly258Val missense_variant 0.21
clpC1 4040517 p.Val63Ala missense_variant 0.35
embC 4239842 c.-21C>A upstream_gene_variant 0.47
embC 4239973 c.111T>G synonymous_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 0.23
embC 4241042 p.Asn394Asp missense_variant 0.27
embC 4242075 p.Arg738Gln missense_variant 0.14
embC 4242425 p.Arg855Gly missense_variant 0.27
embC 4242476 p.Pro872Ala missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 0.9
embC 4242822 p.Val987Gly missense_variant 0.29
embC 4242827 p.Leu989Val missense_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 0.12
ethA 4326439 p.Asn345Lys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.35
gid 4407588 c.615A>G synonymous_variant 0.28
gid 4407780 c.423G>A synonymous_variant 0.21
gid 4407873 c.330G>T synonymous_variant 0.31
gid 4407991 p.Gly71Val missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 0.55