TB-Profiler result

Run: SRR1173195
Summary

Run ID: SRR1173195

Sample name:

Date: 03-04-2023 03:18:49

Number of reads: 544547

Percentage reads mapped: 96.1

Strain: lineage4.4.1.1.1

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
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 0.99
lineage4.4.1.1.1 Euro-American S;Orphans 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.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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 5211 c.-29A>G upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8217 p.Ser306Pro missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777913 p.Ala190Ser missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800767 c.-42C>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472955 n.1110C>A non_coding_transcript_exon_variant 0.22
rrl 1474603 n.946C>T non_coding_transcript_exon_variant 1.0
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170187 p.Glu142Asp missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642427 p.Val298Ala missense_variant 0.2
alr 3841372 p.Gly17Arg missense_variant 0.29
clpC1 4040342 c.363C>G synonymous_variant 0.13
embC 4240726 c.864G>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246978 c.465C>A synonymous_variant 0.17
ubiA 4269133 p.Gly234Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0