TB-Profiler result

Run: SRR1172065
Summary

Run ID: SRR1172065

Sample name:

Date: 03-04-2023 02:55:12

Number of reads: 2872897

Percentage reads mapped: 95.93

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 6741 p.Glu501Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.98 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.88 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2156093 c.18dupA frameshift_variant 1.0 isoniazid
pncA 2288790 c.450_451dupCT frameshift_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.12 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326980 p.Gln165Pro missense_variant 1.0 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 0.99
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 575410 c.65_68delAGGG frameshift_variant 0.28
mshA 575700 c.356dupG frameshift_variant 0.14
mshA 575859 p.Val171Glu missense_variant 0.11
mshA 576161 p.Gly272Arg missense_variant 0.23
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 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.17
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.1
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.1
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.14
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.14
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.11
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.15
rrl 1475626 n.1969T>G non_coding_transcript_exon_variant 0.43
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.11
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.1
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.14
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.1
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.11
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.16
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.17
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.11
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.11
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.11
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.1
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.11
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
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
PPE35 2169320 p.Leu431Phe missense_variant 0.17
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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726116 c.-77T>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087334 c.517dupG frameshift_variant 0.12
ald 3087794 c.976_977dupGA frameshift_variant 0.15
ald 3087892 c.1074_1077dupCCTG frameshift_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269718 p.Ala39Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0