TB-Profiler result

Run: SRR4035823
Summary

Run ID: SRR4035823

Sample name:

Date: 04-04-2023 07:19:13

Number of reads: 1356243

Percentage reads mapped: 99.55

Strain: lineage4.1.2

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 0.99
lineage4.1.2 Euro-American T;H None 0.99
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 6666 p.Gln476Leu missense_variant 0.18
gyrB 6990 p.Asp584Gly missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9364 p.Glu688Val missense_variant 0.14
fgd1 490884 p.Ser34Arg missense_variant 0.12
fgd1 490923 p.Gln47His missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491722 p.Gly314Arg missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762680 c.-690C>T upstream_gene_variant 0.15
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.96
rpoC 765677 p.Arg770Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777173 c.1308C>T synonymous_variant 0.2
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpR5 779131 p.Pro48Ala missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473456 n.-202C>T upstream_gene_variant 0.15
rrl 1473921 n.264A>G non_coding_transcript_exon_variant 0.18
rrl 1474965 n.1308G>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102332 c.711G>A synonymous_variant 0.18
ndh 2102347 c.696G>A synonymous_variant 0.2
ndh 2102699 p.Leu115Pro missense_variant 0.13
katG 2154621 c.1491C>T synonymous_variant 0.17
katG 2154823 p.Leu430Pro missense_variant 0.12
katG 2154944 p.Tyr390His missense_variant 0.14
katG 2155260 c.852C>G synonymous_variant 0.17
katG 2155835 p.Ala93Pro missense_variant 0.12
katG 2156268 c.-157G>A upstream_gene_variant 0.14
PPE35 2170236 p.Phe126Ser missense_variant 0.11
PPE35 2170522 p.Trp31Arg missense_variant 0.15
PPE35 2170529 c.84G>A synonymous_variant 0.18
PPE35 2170538 c.75G>C synonymous_variant 0.18
Rv1979c 2222195 p.Pro324Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223354 c.-190A>T upstream_gene_variant 0.18
Rv1979c 2223360 c.-196G>A upstream_gene_variant 0.18
pncA 2289886 c.-645C>T upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518558 c.446dupG frameshift_variant 0.12
Rv2752c 3066378 c.-187C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086976 p.Ala53Thr missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474981 c.975C>A synonymous_variant 0.18
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
embC 4242255 c.2395delG frameshift_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245458 c.2226G>A synonymous_variant 0.14
embB 4247050 c.537C>T synonymous_variant 0.13
ethA 4326542 p.Glu311Gly missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0