TB-Profiler result

Run: SRR19428551
Summary

Run ID: SRR19428551

Sample name:

Date: 03-04-2023 21:39:54

Number of reads: 405367

Percentage reads mapped: 99.61

Strain: lineage4;lineage3.1.1

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 0.88
lineage4 Euro-American LAM;T;S;X;H None 0.05
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.53
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.83
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8665 c.1366delG frameshift_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.96
mshA 576077 c.730C>T synonymous_variant 0.2
mshA 576183 c.837dupA frameshift_variant 0.11
ccsA 620351 p.Arg154His missense_variant 0.1
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.24
rpoC 763886 c.517C>A synonymous_variant 0.24
rpoC 764509 c.1140G>T synonymous_variant 0.12
rpoC 766796 c.3428delG frameshift_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776409 p.Leu691Pro missense_variant 0.1
mmpL5 776685 p.Ser599Leu missense_variant 0.1
mmpL5 777607 p.Gly292Ser missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801267 c.459A>T synonymous_variant 0.12
fbiC 1304173 p.Val415Met missense_variant 0.17
fbiC 1304422 p.Ala498Thr missense_variant 0.13
fbiC 1305112 p.Asp728Asn missense_variant 0.12
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.15
Rv1258c 1406349 p.Ile331Ser missense_variant 0.63
Rv1258c 1407208 p.Ser45Pro missense_variant 0.11
Rv1258c 1407363 c.-23C>T upstream_gene_variant 0.11
embR 1416577 c.771G>A synonymous_variant 0.11
embR 1417153 c.195C>A synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476471 n.2814G>A non_coding_transcript_exon_variant 0.1
inhA 1674762 c.561T>C synonymous_variant 0.2
inhA 1674902 p.Asp234Gly missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101703 p.Glu447Val missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.75
pncA 2289105 p.Ala46Gly missense_variant 0.12
pncA 2289325 c.-84T>G upstream_gene_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 0.83
pncA 2289969 c.-728G>A upstream_gene_variant 0.12
kasA 2519083 c.969C>A synonymous_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 0.77
Rv2752c 3065711 p.Gly161Ser missense_variant 0.14
Rv2752c 3067008 c.-817C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>A synonymous_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 0.1
Rv3083 3448944 c.441G>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.17
fprA 3474605 p.Arg200Gln missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.1
fbiA 3641219 p.Val226Ala missense_variant 0.12
fbiB 3641304 c.-231C>A upstream_gene_variant 0.1
fbiB 3641914 p.Ala127Asp missense_variant 0.11
alr 3840461 c.960G>T synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 0.18
panD 4044204 c.78G>A synonymous_variant 0.12
embC 4240068 p.Ser69Asn missense_variant 0.12
embC 4240953 p.Ile364Thr missense_variant 0.11
embC 4241562 p.Arg567His missense_variant 0.94
embC 4242075 p.Arg738Gln missense_variant 0.82
embC 4242503 p.Pro881Thr missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.17
embA 4243528 p.Asp99Gly missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.94
gid 4407873 c.330G>T synonymous_variant 0.19