TB-Profiler result

Run: SRR1173062
Summary

Run ID: SRR1173062

Sample name:

Date: 03-04-2023 03:16:14

Number of reads: 7345897

Percentage reads mapped: 73.77

Strain:

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
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 0.93 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2156093 c.18dupA frameshift_variant 1.0 isoniazid
pncA 2288790 c.450_451dupCT frameshift_variant 1.0 pyrazinamide
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576057 c.711_712dupGG frameshift_variant 0.47
mshA 576161 p.Gly272Arg missense_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760866 p.Gly354Cys missense_variant 0.75
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762834 p.Gly1010Cys missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765479 p.Tyr704Asp missense_variant 0.17
rpoC 765556 c.2187G>T synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776078 c.2403C>T synonymous_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778277 c.-713C>T upstream_gene_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304531 p.Ser534Leu missense_variant 0.15
fbiC 1305262 p.His778Asn missense_variant 0.67
embR 1416856 c.492G>T synonymous_variant 0.12
embR 1417258 c.90G>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473205 n.1360T>A non_coding_transcript_exon_variant 0.19
rrl 1475626 n.1969T>G non_coding_transcript_exon_variant 0.15
ndh 2102834 p.Pro70Gln missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155475 p.Lys213Gln missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223304 c.-140G>T upstream_gene_variant 0.4
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289979 c.-743_-739delCGCTG upstream_gene_variant 0.2
eis 2715379 c.-47T>A upstream_gene_variant 0.5
ahpC 2726081 c.-112C>A upstream_gene_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726116 c.-77T>G upstream_gene_variant 1.0
folC 2746927 c.672C>A synonymous_variant 0.33
Rv2752c 3066277 c.-86C>T upstream_gene_variant 0.18
thyX 3067461 p.Leu162Gln missense_variant 0.15
thyA 3074449 p.Leu8Gln missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087892 c.1074_1077dupCCTG frameshift_variant 0.42
Rv3236c 3612360 p.Gly253Trp missense_variant 1.0
rpoA 3878146 p.Pro121Leu missense_variant 0.29
rpoA 3878365 p.Gly48Glu missense_variant 0.15
ddn 3986759 c.-85C>T upstream_gene_variant 0.5
ddn 3987089 c.246G>T synonymous_variant 0.23
clpC1 4038935 c.1770C>A synonymous_variant 0.29
clpC1 4039601 c.1104G>A synonymous_variant 0.33
panD 4044080 p.Val68Leu missense_variant 0.2
panD 4044386 c.-105C>A upstream_gene_variant 0.13
embC 4239842 c.-21C>A upstream_gene_variant 0.15
embC 4241441 p.Pro527Ser missense_variant 1.0
embC 4241755 c.1893C>T synonymous_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242813 p.Asp984Val missense_variant 0.13
embA 4246073 p.Asn947Lys missense_variant 0.33
aftB 4267083 p.His585Leu missense_variant 0.23
aftB 4267468 p.Tyr457Asn missense_variant 0.25
aftB 4268620 p.Val73Leu missense_variant 0.25
ethA 4326190 p.Glu428Asp missense_variant 0.13
ethA 4327203 p.Met91Leu missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408185 c.18C>A synonymous_variant 0.12
gid 4408382 c.-180A>C upstream_gene_variant 0.18