TB-Profiler result

Run: SRR19428603
Summary

Run ID: SRR19428603

Sample name:

Date: 03-04-2023 21:41:50

Number of reads: 601131

Percentage reads mapped: 99.59

Strain: lineage4.3.4;lineage3.1.1;lineage1.1.2

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
lineage3 East-African-Indian CAS RD750 0.72
lineage4 Euro-American LAM;T;S;X;H None 0.14
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.08
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.5
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.1
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.54
lineage4.3.4 Euro-American (LAM) LAM RD174 0.07
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 0.25
gyrB 6124 c.885C>T synonymous_variant 0.24
gyrB 6140 p.Val301Leu missense_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.43
gyrA 8503 p.Leu401Arg missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.86
mshA 575241 c.-107_-106insG upstream_gene_variant 0.1
mshA 576020 p.Ile225Val missense_variant 0.1
rpoB 759746 c.-61C>T upstream_gene_variant 0.55
rpoC 762434 c.-936T>G upstream_gene_variant 0.83
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 763884 p.Ala172Val missense_variant 0.19
rpoC 763886 c.517C>A synonymous_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776007 p.His825Arg missense_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779267 c.280dupC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.21
embR 1416367 c.981C>A synonymous_variant 0.1
embR 1417019 p.Cys110Tyr missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.14
rrl 1473763 n.106C>T non_coding_transcript_exon_variant 0.11
tlyA 1917777 c.-163A>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154435 c.1677T>C synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 0.73
PPE35 2167926 p.Leu896Ser missense_variant 0.74
PPE35 2167983 p.Gly877Asp missense_variant 0.2
PPE35 2170066 p.Ala183Thr missense_variant 0.14
PPE35 2170461 p.Gly51Glu missense_variant 0.38
Rv1979c 2221783 p.Ala461Glu missense_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.64
pncA 2289365 c.-125delC upstream_gene_variant 0.84
kasA 2518132 c.18C>T synonymous_variant 0.14
eis 2714908 p.Val142Gly missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 0.66
ahpC 2726672 c.480G>A synonymous_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 0.14
Rv2752c 3066279 c.-88delA upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474076 p.Lys24Glu missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 0.15
fbiB 3641746 p.Asp71Gly missense_variant 0.11
alr 3840492 p.Leu310Pro missense_variant 0.15
alr 3840719 c.702A>G synonymous_variant 0.11
rpoA 3878622 c.-115C>G upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.15
embC 4240172 p.Val104Met missense_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 0.19
embC 4241042 p.Asn394Asp missense_variant 0.17
embC 4241562 p.Arg567His missense_variant 0.45
embC 4242075 p.Arg738Gln missense_variant 0.52
embA 4242481 c.-752C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242680 c.2820delC frameshift_variant 0.22
embC 4242761 c.2902delG frameshift_variant 0.14
embA 4243848 p.Val206Met missense_variant 0.13
embA 4244999 c.1767G>C synonymous_variant 0.1
embA 4245883 p.Gly884Asp missense_variant 0.28
embA 4245969 p.Pro913Ser missense_variant 0.11
embA 4246468 c.3238_3239delAC frameshift_variant 0.12
embB 4247827 c.1314C>T synonymous_variant 0.12
aftB 4267671 p.Ala389Val missense_variant 0.11
aftB 4267933 p.Ala302Pro missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.13
aftB 4269606 c.-770T>C upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.17
whiB6 4338649 c.-128C>T upstream_gene_variant 0.43
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407873 c.330G>T synonymous_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.17