TB-Profiler result

Run: ERR9030453
Summary

Run ID: ERR9030453

Sample name:

Date: 02-04-2023 09:26:51

Number of reads: 1692866

Percentage reads mapped: 99.95

Strain: lineage3.1.1

Drug-resistance: RR-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 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 1.0
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 761082 c.1279_1284delACCAGC conservative_inframe_deletion 1.0 rifampicin
pncA 2289043 p.Ser67Pro missense_variant 1.0 pyrazinamide
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 7544 p.Met81Ile missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576286 c.939C>A synonymous_variant 0.15
mshA 576413 p.Gly356Cys missense_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762639 p.Gly945Trp missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764944 p.His525Gln missense_variant 0.98
rpoC 766111 c.2742G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304425 p.Leu499Met missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474980 n.1323G>T non_coding_transcript_exon_variant 0.18
rrl 1475027 n.1370G>T non_coding_transcript_exon_variant 0.18
rrl 1475105 n.1448G>T non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918090 p.Ala51Pro missense_variant 0.67
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154851 p.Gly421Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170144 p.Gly157Trp missense_variant 0.15
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 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519178 p.Ser355Leu missense_variant 0.17
eis 2714786 p.Arg183Ser missense_variant 0.13
eis 2715134 c.199C>T synonymous_variant 0.2
eis 2715525 c.-193G>T upstream_gene_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859534 c.884delG frameshift_variant 0.18
ribD 2987342 c.504C>T synonymous_variant 0.22
Rv2752c 3066286 c.-95C>A upstream_gene_variant 0.15
Rv2752c 3067060 c.-869C>A upstream_gene_variant 0.18
thyX 3067421 c.525G>T synonymous_variant 0.5
thyX 3067592 c.354G>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339336 c.219C>A synonymous_variant 0.2
Rv3083 3448387 c.-117C>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641559 p.Ala9Thr missense_variant 0.13
fbiB 3641628 p.Ala32Ser missense_variant 0.17
fbiB 3642174 p.Val214Met missense_variant 0.67
rpoA 3878583 c.-76C>A upstream_gene_variant 0.22
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241116 c.1254C>T synonymous_variant 0.14
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242633 p.Pro924Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243518 p.Gly96Ser missense_variant 0.5
embA 4243700 c.468C>A synonymous_variant 0.18
embA 4244192 c.960C>T synonymous_variant 0.18
embA 4244968 p.Gly579Val missense_variant 0.15
embA 4245892 p.Ile887Thr missense_variant 0.11
embB 4247197 c.684C>A synonymous_variant 0.22
embB 4248631 c.2118G>T synonymous_variant 0.33
aftB 4267910 c.927G>T synonymous_variant 0.2
aftB 4267983 p.Arg285His missense_variant 0.15
aftB 4268275 p.Glu188Lys missense_variant 0.12
aftB 4268911 c.-75G>A upstream_gene_variant 0.13
aftB 4268917 c.-81C>A upstream_gene_variant 0.12
ubiA 4268971 p.Ala288Glu missense_variant 0.14
ubiA 4269993 c.-160A>G upstream_gene_variant 0.11
whiB6 4338257 p.Ala89Thr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98