TB-Profiler result

Run: SRR3732621
Summary

Run ID: SRR3732621

Sample name:

Date: 04-04-2023 05:36:45

Number of reads: 1727925

Percentage reads mapped: 99.57

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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 5349 p.Thr37Ile missense_variant 0.13
gyrB 6195 p.Gly319Val missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491192 p.Gly137Glu missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491725 p.His315Tyr missense_variant 0.11
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575958 p.Gln204Arg missense_variant 0.14
ccsA 620651 p.Ala254Asp missense_variant 0.12
ccsA 620835 c.945C>T synonymous_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762503 c.-867G>T upstream_gene_variant 0.12
rpoC 763683 p.Trp105Leu missense_variant 0.13
rpoC 764043 p.Thr225Asn missense_variant 0.12
rpoC 764216 p.Asn283Asp missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776288 c.2193C>A synonymous_variant 0.12
mmpL5 776348 c.2133G>T synonymous_variant 0.14
mmpL5 777019 p.Asp488His missense_variant 0.12
mmpL5 777106 p.Ser459Pro missense_variant 0.11
mmpL5 777119 p.His454Gln missense_variant 0.14
mmpL5 777122 c.1359C>T synonymous_variant 0.11
mmpL5 779370 c.-890G>A upstream_gene_variant 0.33
mmpS5 779648 c.-743C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800727 c.-82C>T upstream_gene_variant 0.15
Rv1258c 1406556 p.Trp262Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471974 n.129T>A non_coding_transcript_exon_variant 0.25
rrs 1472104 n.259G>T non_coding_transcript_exon_variant 0.22
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.67
rrl 1475450 n.1793C>A non_coding_transcript_exon_variant 0.4
rrl 1476709 n.3052C>A non_coding_transcript_exon_variant 0.25
inhA 1673586 c.-616C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.12
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2169426 p.Pro396Gln missense_variant 0.12
PPE35 2169581 c.1032C>G synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289826 c.-585A>T upstream_gene_variant 0.2
pncA 2290224 c.-983A>G upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714354 p.Gly327Ser missense_variant 0.19
thyX 3067415 c.530delA frameshift_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339608 p.Pro164Leu missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474990 c.984C>A synonymous_variant 0.14
fbiB 3642847 p.Pro438Leu missense_variant 0.15
rpoA 3878695 c.-189dupT upstream_gene_variant 0.18
clpC1 4038443 c.2262G>T synonymous_variant 0.12
clpC1 4039998 p.Gly236Asp missense_variant 0.12
clpC1 4040247 p.Ala153Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245960 p.Gln910Lys missense_variant 1.0
aftB 4268615 c.222C>T synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.14