TB-Profiler result

Run: SRR12199428
Summary

Run ID: SRR12199428

Sample name:

Date: 03-04-2023 06:39:05

Number of reads: 96361

Percentage reads mapped: 87.11

Strain: lineage4.9;lineage1.1

Drug-resistance: Sensitive

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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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.14
lineage4.9 Euro-American (H37Rv-like) T1 None 0.96
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
fgd1 491663 p.Val294Ala missense_variant 0.4
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764015 p.Leu216Met missense_variant 0.4
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303500 p.His190Gln missense_variant 0.4
Rv1258c 1407244 p.Leu33Val missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472158 n.313C>A non_coding_transcript_exon_variant 0.4
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.29
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.29
rrl 1475547 n.1890A>T non_coding_transcript_exon_variant 0.22
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.33
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.33
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.29
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.29
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.4
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.29
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.29
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.29
rrl 1475880 n.2223C>G non_coding_transcript_exon_variant 0.29
rrl 1475881 n.2224T>G non_coding_transcript_exon_variant 0.29
rrl 1475882 n.2225C>G non_coding_transcript_exon_variant 0.29
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.29
rrl 1476176 n.2519C>G non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169500 p.Met371Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.71
PPE35 2170053 p.Thr187Ser missense_variant 0.71
kasA 2518071 c.-44G>T upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715160 p.Val58Gly missense_variant 0.5
eis 2715274 p.Ala20Val missense_variant 0.22
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
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612776 p.Asp114Ala missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841529 c.-109C>A upstream_gene_variant 0.25
clpC1 4040517 p.Val63Ala missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4248955 c.2442C>T synonymous_variant 0.67
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0