TB-Profiler result

Run: SRR13423613
Summary

Run ID: SRR13423613

Sample name:

Date: 03-04-2023 08:54:24

Number of reads: 778274

Percentage reads mapped: 99.3

Strain: lineage4.4.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 None 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2154507 c.1604dupA frameshift_variant 1.0 isoniazid
pncA 2288953 p.Gly97Ser missense_variant 0.88 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
gid 4407731 c.471delG frameshift_variant 1.0 streptomycin
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 8630 c.1329G>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576173 p.Pro276Ser missense_variant 0.11
rpoB 761279 c.1473C>T synonymous_variant 0.17
rpoB 762378 p.Gly858Cys missense_variant 0.12
rpoB 762453 p.His883Tyr missense_variant 0.13
rpoC 763662 p.Ala98Val missense_variant 0.12
rpoC 765659 p.Ala764Thr missense_variant 0.14
rpoC 766368 p.Ala1000Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776238 p.Gly748Asp missense_variant 0.15
mmpS5 778533 p.Glu125* stop_gained 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407414 c.-74G>A upstream_gene_variant 0.12
embR 1416864 p.Phe162Leu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473304 n.1460delG non_coding_transcript_exon_variant 0.29
fabG1 1673312 c.-128C>A upstream_gene_variant 0.12
rpsA 1833927 p.Thr129Met missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102101 c.942C>T synonymous_variant 0.11
ndh 2102108 p.Pro312His missense_variant 0.13
ndh 2102820 p.Val75Met missense_variant 0.13
katG 2154442 p.Lys557Met missense_variant 0.12
katG 2154561 c.1551C>T synonymous_variant 0.14
katG 2155030 p.Ala361Val missense_variant 0.12
PPE35 2168100 c.2512dupC frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290010 c.-770delC upstream_gene_variant 0.12
ahpC 2726419 p.Glu76Gly missense_variant 0.11
Rv2752c 3065009 p.Pro395Ser missense_variant 0.12
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449054 p.Gly184Asp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612093 p.Gly342Trp missense_variant 0.12
Rv3236c 3612718 c.399C>T synonymous_variant 0.13
rpoA 3878643 c.-136G>T upstream_gene_variant 0.12
clpC1 4039739 c.966C>A synonymous_variant 0.14
clpC1 4040838 c.-134C>T upstream_gene_variant 0.12
embC 4239963 p.Val34Ala missense_variant 0.18
embC 4240191 p.Pro110His missense_variant 0.12
embC 4241303 p.Thr481Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 1.0
embA 4245957 p.Gly909Arg missense_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4248519 p.Ser669Ile missense_variant 0.2
embB 4249168 c.2655C>A synonymous_variant 0.11
aftB 4267431 p.Ser469Leu missense_variant 0.11
aftB 4267540 p.Pro433Ser missense_variant 0.15
aftB 4268027 c.809delT frameshift_variant 0.11
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ethA 4327572 c.-99C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407884 p.Asp107Tyr missense_variant 0.13