TB-Profiler result

Run: SRR1174291
Summary

Run ID: SRR1174291

Sample name:

Date: 03-04-2023 03:33:56

Number of reads: 1009150

Percentage reads mapped: 57.81

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
katG 2155693 p.Ser140Asn missense_variant 0.2 isoniazid
ethA 4326236 p.Gly413Asp missense_variant 1.0 ethionamide
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 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576443 p.Gly366Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.54
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.56
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.54
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.53
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.56
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.38
rrs 1472252 n.407G>C non_coding_transcript_exon_variant 0.36
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.36
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.36
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.36
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.57
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.54
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.51
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.53
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.53
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.49
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.22
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.16
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.11
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.1
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.11
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.11
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.11
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.11
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.12
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.21
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.21
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.21
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.2
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.26
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.44
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.51
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.51
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.51
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.51
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.52
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.51
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.53
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.54
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.55
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.71
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.69
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.68
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.62
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.56
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.59
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.59
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.59
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.55
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.56
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.56
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.51
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155674 c.438G>T synonymous_variant 0.22
katG 2155691 c.421T>C synonymous_variant 0.2
katG 2155696 p.Ala139Gly missense_variant 0.21
katG 2155704 c.408C>G synonymous_variant 0.24
katG 2155716 c.396T>C synonymous_variant 0.22
katG 2155722 c.390G>C synonymous_variant 0.25
katG 2155728 c.384G>T synonymous_variant 0.27
katG 2155734 p.Met126Asn missense_variant 0.27
katG 2155741 p.Gly124Thr missense_variant 0.25
katG 2155743 p.Gly123Ser missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448771 p.Thr90Ala missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568507 p.Gln58Arg missense_variant 0.96
fbiA 3640958 p.Gly139Asp missense_variant 1.0
alr 3841174 p.Gly83Arg missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338441 p.Tyr27* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0