TB-Profiler result

Run: SRR3105787
Summary

Run ID: SRR3105787

Sample name:

Date: 04-04-2023 05:09:22

Number of reads: 264406

Percentage reads mapped: 99.3

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
gyrA 7582 p.Asp94Gly missense_variant 0.88 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288928 p.Gly105Asp missense_variant 0.8 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 0.4 ethambutol
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
gyrB 6112 p.Met291Ile missense_variant 0.75
gyrB 6124 c.885C>T synonymous_variant 0.6
gyrA 7282 c.-20C>A upstream_gene_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.38
gyrA 8948 c.1647G>A synonymous_variant 0.62
gyrA 9143 c.1842T>C synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 0.71
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.75
rpoC 763886 c.517C>A synonymous_variant 0.75
rpoC 767123 p.Val1252Leu missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.43
mmpR5 779474 p.Gly162Glu missense_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474604 n.947G>A non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156135 c.-24A>G upstream_gene_variant 0.5
PPE35 2169485 c.1120_1127delGTTGGGAA frameshift_variant 0.67
Rv1979c 2222418 p.Asp249Glu missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.43
pncA 2289365 c.-125delC upstream_gene_variant 0.5
kasA 2518132 c.18C>T synonymous_variant 0.57
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.29
folC 2746213 c.1386G>A synonymous_variant 1.0
Rv2752c 3065065 p.Ala376Gly missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474366 c.360G>T synonymous_variant 0.67
fprA 3475159 p.Asn385Asp missense_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244363 p.Asn377Lys missense_variant 0.22
embB 4246907 p.Ile132Val missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 0.6
ubiA 4269387 p.Glu149Asp missense_variant 0.5
whiB6 4338290 c.231delA frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.33
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.38