TB-Profiler result

Run: SRR5535909
Summary

Run ID: SRR5535909

Sample name:

Date: 04-04-2023 10:44:16

Number of reads: 2149814

Percentage reads mapped: 98.95

Strain: lineage3.1.1

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 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
pncA 2284492 c.-447_*4188del transcript_ablation 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 7585 p.Ser95Thr missense_variant 1.0
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 760062 p.Glu86* stop_gained 0.18
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 766482 p.Arg1038Leu missense_variant 0.18
rpoC 767123 p.Val1252Met missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775874 c.2607C>A synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778677 p.Lys77Gln missense_variant 0.29
mmpR5 779149 p.Glu54* stop_gained 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417294 c.54A>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473119 n.1274C>A non_coding_transcript_exon_variant 0.33
rrl 1475262 n.1605G>T non_coding_transcript_exon_variant 0.4
rrl 1475440 n.1783T>G non_coding_transcript_exon_variant 0.4
rrl 1475568 n.1911A>C non_coding_transcript_exon_variant 0.5
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.33
rpsA 1833898 c.357C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918006 p.Ala23Ser missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168130 p.Pro828Gln missense_variant 0.29
PPE35 2168134 p.Asp827Tyr missense_variant 0.29
PPE35 2168901 p.Pro571Leu missense_variant 0.33
PPE35 2169553 p.Pro354Ser missense_variant 0.17
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726761 p.Leu190Arg missense_variant 0.12
folC 2746620 p.Arg327Trp missense_variant 0.12
ribD 2986854 p.Gln6Lys missense_variant 0.12
thyA 3073985 p.Leu163Ile missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448618 p.Glu39* stop_gained 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877754 p.Asp252Tyr missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240661 p.Trp267Gly missense_variant 0.33
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245079 p.Trp616Leu missense_variant 0.19
embA 4245275 c.2043C>A synonymous_variant 0.13
ubiA 4269311 p.Trp175Gly missense_variant 1.0
whiB6 4338594 c.-73T>G upstream_gene_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0