TB-Profiler result

Run: SRR4035807
Summary

Run ID: SRR4035807

Sample name:

Date: 18-08-2022 14:03:18

Number of reads: 817043

Percentage reads mapped: 99.52

Strain: lineage4.1.2

Drug-resistance: HR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.98
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
katG 2156024 c.87delC frameshift_variant 0.12 isoniazid
ethA 4326609 c.864delC frameshift_variant 0.13 ethionamide
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 5715 p.Lys159Met missense_variant 0.17
gyrB 6145 c.906C>T synonymous_variant 0.14
gyrB 6180 p.Gly314Asp missense_variant 0.14
gyrA 8372 c.1071G>A synonymous_variant 0.14
gyrA 8727 p.Arg476Cys missense_variant 0.18
gyrA 9306 p.Asp669His missense_variant 0.18
gyrA 9370 p.Leu690Pro missense_variant 0.2
fgd1 490747 c.-36C>T upstream_gene_variant 0.15
fgd1 491280 c.498C>T synonymous_variant 0.18
fgd1 491299 p.Tyr173Asn missense_variant 0.18
fgd1 491418 c.636A>G synonymous_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575300 c.-48A>T upstream_gene_variant 0.14
mshA 576069 p.Gly241Val missense_variant 0.16
mshA 576317 p.Arg324Trp missense_variant 0.2
rpoB 759908 c.102C>T synonymous_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 0.92
rpoB 761061 p.Ala419Thr missense_variant 0.14
rpoB 761099 c.1293C>T synonymous_variant 0.14
rpoB 761288 c.1482G>A synonymous_variant 0.13
rpoC 763700 p.Pro111Ser missense_variant 0.12
rpoC 763709 c.341dupT frameshift_variant 0.13
rpoC 763838 p.Val157Met missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 0.94
rpoC 764344 c.975C>T synonymous_variant 0.13
rpoC 764590 p.Lys407Asn missense_variant 0.15
rpsL 781365 c.-195T>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781402 c.-158A>T upstream_gene_variant 0.14
rpsL 781834 p.Gly92Ala missense_variant 0.14
rplC 800926 p.Arg40Gly missense_variant 0.11
rplC 801075 c.267G>T synonymous_variant 0.13
fbiC 1303121 p.Arg64Gln missense_variant 0.15
fbiC 1303132 p.Ala68Thr missense_variant 0.15
fbiC 1303735 p.Glu269Lys missense_variant 0.15
fbiC 1303740 c.810C>T synonymous_variant 0.18
fbiC 1304142 c.1212G>A synonymous_variant 0.18
fbiC 1305142 p.Glu738* stop_gained 0.15
fbiC 1305248 p.Ala773Val missense_variant 0.14
atpE 1460940 c.-105C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673400 c.-40C>T upstream_gene_variant 0.17
inhA 1673715 c.-487C>G upstream_gene_variant 0.15
inhA 1674675 c.474C>T synonymous_variant 0.17
inhA 1674686 p.Thr162Met missense_variant 0.17
rpsA 1833475 c.-67G>A upstream_gene_variant 0.14
rpsA 1833854 p.Lys105Glu missense_variant 0.15
rpsA 1834715 p.Phe392Ile missense_variant 0.15
tlyA 1917945 c.6A>G synonymous_variant 0.18
tlyA 1917953 p.Ala5Val missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155576 p.Lys179Arg missense_variant 0.12
pncA 2289884 c.-643G>A upstream_gene_variant 0.18
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518135 c.21T>C synonymous_variant 0.1
kasA 2519049 p.Gly312Asp missense_variant 0.17
eis 2714761 p.Leu191Pro missense_variant 0.18
eis 2715450 c.-118T>C upstream_gene_variant 0.12
ahpC 2726083 c.-110G>A upstream_gene_variant 0.2
ahpC 2726732 p.Lys180Asn missense_variant 0.14
folC 2747241 p.Tyr120Asn missense_variant 0.13
folC 2747608 c.-10C>A upstream_gene_variant 0.17
pepQ 2860444 c.-26C>T upstream_gene_variant 0.14
thyX 3067796 c.150C>T synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087291 p.Val158Met missense_variant 0.17
fbiA 3641331 c.793delG frameshift_variant 0.2
fbiB 3641407 c.-128C>T upstream_gene_variant 0.13
fbiA 3641428 p.Ala296Thr missense_variant 0.15
fbiB 3642202 p.Ser223Phe missense_variant 0.2
fbiB 3642648 p.Met372Val missense_variant 0.18
panD 4044010 p.Ala91Glu missense_variant 0.17
panD 4044258 c.24G>C synonymous_variant 0.17
embC 4240966 c.1104G>A synonymous_variant 0.14
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244197 p.Val322Ala missense_variant 0.15
embA 4244626 p.Leu465Pro missense_variant 0.17
embB 4245869 c.-645C>A upstream_gene_variant 0.14
embB 4247646 p.Glu378Gly missense_variant 0.12
embB 4247653 c.1140C>T synonymous_variant 0.13
embB 4247765 c.1252C>T synonymous_variant 0.14
embB 4249427 p.Arg972Cys missense_variant 0.17
embB 4249735 c.3222T>A synonymous_variant 0.13
ubiA 4269656 p.Val60Leu missense_variant 0.15
ubiA 4269671 p.Val55Leu missense_variant 0.13
ubiA 4269905 c.-72G>A upstream_gene_variant 0.13
ethA 4326063 p.Gly471Ser missense_variant 0.15
ethA 4326177 p.Glu433Gln missense_variant 0.18
gid 4407849 c.354C>T synonymous_variant 0.17
gid 4408311 c.-109C>T upstream_gene_variant 0.18