TB-Profiler result

Run: SRR6797373
Summary

Run ID: SRR6797373

Sample name:

Date: 04-04-2023 16:07:53

Number of reads: 2971231

Percentage reads mapped: 99.08

Strain: lineage4.2.2.2;lineage1.1.3

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 0.21
lineage1 Indo-Oceanic EAI RD239 0.8
lineage4.2 Euro-American H;T;LAM None 0.22
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.8
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.23
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.78
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.26
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
gid 4408100 c.102delG frameshift_variant 0.22 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 0.77
gyrA 7323 p.Pro8Ser missense_variant 0.62
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.74
gyrA 8688 p.Ala463Ser missense_variant 0.26
gyrA 9143 c.1842T>C synonymous_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491448 c.666C>T synonymous_variant 0.85
fgd1 491742 c.960T>C synonymous_variant 0.8
mshA 576077 c.730C>T synonymous_variant 0.18
mshA 576675 p.Arg443His missense_variant 0.81
rpoC 763031 c.-339T>C upstream_gene_variant 0.87
rpoC 763884 p.Ala172Val missense_variant 0.84
rpoC 763886 c.517C>A synonymous_variant 0.83
rpoC 765171 p.Pro601Leu missense_variant 0.89
rpoC 765230 p.Ala621Thr missense_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.86
mmpL5 778099 p.Asp128Asn missense_variant 0.8
mmpS5 778581 p.Gly109Ser missense_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.79
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474990 n.1333C>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.72
PPE35 2167926 p.Leu896Ser missense_variant 0.72
PPE35 2167983 p.Gly877Asp missense_variant 0.75
Rv1979c 2222308 p.Asp286Gly missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.77
ahpC 2726051 c.-142G>A upstream_gene_variant 0.78
Rv2752c 3064632 c.1560C>T synonymous_variant 0.79
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.18
thyX 3068043 c.-98A>G upstream_gene_variant 0.81
ald 3086742 c.-78A>C upstream_gene_variant 0.24
ald 3086767 c.-53A>T upstream_gene_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.81
fprA 3475159 p.Asn385Asp missense_variant 0.89
clpC1 4040231 c.474C>T synonymous_variant 0.82
clpC1 4040517 p.Val63Ala missense_variant 0.74
embC 4240671 p.Thr270Ile missense_variant 0.9
embC 4241042 p.Asn394Asp missense_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.78
embA 4245314 c.2082G>C synonymous_variant 0.75
embA 4245969 p.Pro913Ser missense_variant 0.76
embB 4247396 p.Ala295Thr missense_variant 0.77
embB 4247646 p.Glu378Ala missense_variant 0.77
ubiA 4269387 p.Glu149Asp missense_variant 0.72
aftB 4269606 c.-770T>C upstream_gene_variant 0.72
ethA 4326402 p.Gly358Arg missense_variant 0.66
whiB6 4338308 c.213dupT frameshift_variant 0.84
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.58
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407780 c.423G>A synonymous_variant 0.79
gid 4407873 c.330G>T synonymous_variant 0.83