TB-Profiler result

Run: SRR1180179
Summary

Run ID: SRR1180179

Sample name:

Date: 03-04-2023 03:53:18

Number of reads: 2846039

Percentage reads mapped: 87.01

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 0.95 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.87 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2156093 c.18dupA frameshift_variant 1.0 isoniazid
pncA 2288790 c.450_451dupCT frameshift_variant 0.97 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.28 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326980 p.Gln165Pro missense_variant 0.99 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
mshA 576161 p.Gly272Arg missense_variant 0.27
mshA 576217 c.873dupC frameshift_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761963 c.2157G>C synonymous_variant 0.11
rpoB 761974 p.His723Leu missense_variant 0.11
rpoB 762003 p.Asn733Gln missense_variant 0.12
rpoB 762009 p.Leu735Met missense_variant 0.11
rpoB 762015 p.Glu737Ser missense_variant 0.12
rpoB 762026 c.2220G>C synonymous_variant 0.15
rpoB 762053 c.2247T>C synonymous_variant 0.15
rpoB 762057 p.Ile751Val missense_variant 0.12
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 0.2
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.13
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.1
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.12
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.16
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.15
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.15
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.18
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.14
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.15
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.13
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.15
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.14
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.16
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.15
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.2
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.2
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.12
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.14
rrl 1475626 n.1969T>G non_coding_transcript_exon_variant 0.41
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.16
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.98
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99
ahpC 2726116 c.-77T>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087794 c.976_977dupGA frameshift_variant 0.17
ald 3087892 c.1074_1077dupCCTG frameshift_variant 0.37
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4038845 c.1860G>C synonymous_variant 0.11
clpC1 4038854 p.Lys617Arg missense_variant 0.12
clpC1 4038860 c.1845G>C synonymous_variant 0.25
clpC1 4038863 c.1842G>C synonymous_variant 0.22
clpC1 4038878 c.1827A>G synonymous_variant 0.25
clpC1 4038899 c.1806C>G synonymous_variant 0.2
clpC1 4038905 c.1800A>C synonymous_variant 0.17
clpC1 4038911 c.1794G>T synonymous_variant 0.12
embC 4240221 c.368_370dupTGC disruptive_inframe_insertion 0.16
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