TB-Profiler result

Run: SRR3105776
Summary

Run ID: SRR3105776

Sample name:

Date: 04-04-2023 05:08:56

Number of reads: 1418530

Percentage reads mapped: 95.79

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 0.96
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.96
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.98
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.17 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288824 c.417dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4249583 p.Asp1024Asn missense_variant 0.94 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 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8234 c.933T>G synonymous_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576520 c.1176delG frameshift_variant 0.25
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 762534 p.Ile910Leu missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 0.91
rpoC 766415 p.His1016Asn missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 777649 p.Ala278Pro missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472042 n.197T>G non_coding_transcript_exon_variant 0.22
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.17
rrs 1472504 n.659A>T non_coding_transcript_exon_variant 0.27
rrs 1472512 n.667A>G non_coding_transcript_exon_variant 0.57
rrs 1472683 n.838_839insTA non_coding_transcript_exon_variant 0.36
rrl 1475697 n.2040C>T non_coding_transcript_exon_variant 0.9
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.4
inhA 1674952 p.Pro251Ala missense_variant 0.4
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 2167983 p.Gly877Asp missense_variant 0.9
PPE35 2169320 p.Leu431Phe missense_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.89
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86
ahpC 2726338 p.Val49Gly missense_variant 0.29
ribD 2987307 p.Ala157Pro missense_variant 0.31
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067995 c.-50A>C upstream_gene_variant 0.22
thyA 3074595 c.-124C>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568732 c.-53C>T upstream_gene_variant 0.92
clpC1 4039932 p.Gly258Val missense_variant 0.43
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 0.92
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.62
embA 4243848 p.Val206Met missense_variant 0.95
embA 4245218 c.1986C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246800 p.Gly96Val missense_variant 0.28
embB 4247646 p.Glu378Ala missense_variant 0.89
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.18
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.89
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408052 p.Asn51Asp missense_variant 1.0
gid 4408170 c.33C>T synonymous_variant 1.0