TB-Profiler result

Run: SRR4037706
Summary

Run ID: SRR4037706

Sample name:

Date: 04-04-2023 07:36:25

Number of reads: 509041

Percentage reads mapped: 99.65

Strain: lineage4.4.1

Drug-resistance: Sensitive

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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 0.97
lineage4.4.1 Euro-American (S-type) S;T None 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
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 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491677 p.Gln299* stop_gained 0.2
rpoB 760022 c.216T>G synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpR5 778202 c.-788G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305478 p.Thr850Ser missense_variant 0.13
Rv1258c 1406375 c.966C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.12
rrl 1475303 n.1646G>C non_coding_transcript_exon_variant 0.17
inhA 1673363 c.-839G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155195 p.Thr306Ile missense_variant 0.25
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2168671 p.Gly648Ser missense_variant 0.17
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.5
Rv2752c 3066175 p.Pro6Arg missense_variant 0.9
thyX 3067734 p.Ser71* stop_gained 0.17
thyA 3073806 c.666C>G synonymous_variant 0.5
thyA 3074268 c.204T>C synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474261 c.255C>T synonymous_variant 0.22
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338177 c.345G>A synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0