TB-Profiler result

Run: SRR4035549
Summary

Run ID: SRR4035549

Sample name:

Date: 04-04-2023 07:10:14

Number of reads: 940126

Percentage reads mapped: 99.39

Strain: lineage3

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 0.99
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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155149 p.Trp321Cys missense_variant 0.12 isoniazid
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 5656 c.417C>A synonymous_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7899 p.Ala200Thr missense_variant 0.14
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 8870 c.1569G>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760545 p.Gly247Trp missense_variant 0.17
rpoB 761055 p.Val417Phe missense_variant 0.22
rpoB 761970 p.Gly722Cys missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762623 p.Lys939Asn missense_variant 0.14
rpoB 762926 c.3123delG frameshift_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775609 c.2868_2871delATCG frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777041 c.1440G>T synonymous_variant 0.17
mmpL5 777780 p.Thr234Arg missense_variant 0.25
mmpR5 777992 c.-998G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781718 c.159C>A synonymous_variant 0.12
rplC 800991 p.Lys61Asn missense_variant 0.14
fbiC 1304807 p.Pro626His missense_variant 0.12
fbiC 1304832 c.1902C>T synonymous_variant 0.12
fbiC 1305372 p.Glu814Asp missense_variant 0.18
embR 1416659 c.688delC frameshift_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473580 n.-78G>T upstream_gene_variant 0.12
rrl 1475793 n.2139delA non_coding_transcript_exon_variant 0.12
inhA 1674304 p.Gln35Lys missense_variant 0.12
rpsA 1833507 c.-35C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918201 p.Asp88Tyr missense_variant 0.18
ndh 2101913 c.1129delT frameshift_variant 0.2
ndh 2103114 c.-72G>T upstream_gene_variant 0.13
ndh 2103214 c.-172T>G upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156487 c.-377delC upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290189 c.-948G>A upstream_gene_variant 0.12
kasA 2518110 c.-5T>G upstream_gene_variant 0.15
ahpC 2725954 c.-239C>T upstream_gene_variant 0.16
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.32
pepQ 2859720 p.Met233Ile missense_variant 0.14
pepQ 2859816 c.603G>A synonymous_variant 0.14
pepQ 2860245 c.174C>A synonymous_variant 0.25
ribD 2986800 c.-39T>C upstream_gene_variant 0.1
ribD 2987307 p.Ala157Pro missense_variant 0.18
Rv2752c 3064663 p.Lys510Arg missense_variant 0.14
Rv2752c 3064985 c.1207C>T synonymous_variant 0.12
Rv2752c 3065673 p.Phe173Leu missense_variant 0.15
thyA 3073806 c.666C>G synonymous_variant 0.29
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449054 p.Gly184Asp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474179 p.Pro58His missense_variant 0.13
fprA 3474658 p.Leu218Ile missense_variant 0.18
fbiB 3642622 p.Ala363Val missense_variant 0.12
clpC1 4038292 p.Asp805Tyr missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243745 c.513C>A synonymous_variant 0.14
aftB 4268770 p.Gln23* stop_gained 0.29
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338312 c.210G>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0