TB-Profiler result

Run: SRR14179705
Summary

Run ID: SRR14179705

Sample name:

Date: 03-04-2023 10:18:27

Number of reads: 23314303

Percentage reads mapped: 91.07

Strain: lineage3

Drug-resistance: Pre-XDR-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
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
gyrB 6575 p.Arg446Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
tlyA 1918640 c.704dupG frameshift_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288919 p.Gly108Glu missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326734 c.739dupG frameshift_variant 1.0 ethionamide, 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
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
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.1
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.1
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.1
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.11
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.1
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.1
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.11
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.1
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.1
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.1
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.1
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.1
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.12
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.11
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.14
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.14
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.14
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.13
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
inhA 1673406 c.-796C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065232 c.951_959delAATGTCGCG disruptive_inframe_deletion 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242083 c.2221C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0