TB-Profiler result

Run: SRR4034317
Summary

Run ID: SRR4034317

Sample name:

Date: 04-04-2023 06:42:47

Number of reads: 525011

Percentage reads mapped: 99.49

Strain: lineage4.1.2

Drug-resistance: Other

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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 0.98
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
pncA 2288896 c.345delA frameshift_variant 0.22 pyrazinamide
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 5184 c.-56A>G upstream_gene_variant 0.2
gyrB 6308 p.Val357Leu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7736 c.435C>A synonymous_variant 0.29
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8884 p.Arg528His missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575519 p.Ala58Thr missense_variant 0.14
mshA 576628 c.1281G>A synonymous_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761487 p.Glu561* stop_gained 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766778 p.Glu1137* stop_gained 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777933 p.Lys183Arg missense_variant 0.2
mmpR5 778055 c.-935G>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781915 p.Ala119Asp missense_variant 0.14
fbiC 1303821 c.892_893delAA frameshift_variant 0.2
fbiC 1305288 c.2358C>A synonymous_variant 0.29
Rv1258c 1406185 p.Pro386Ser missense_variant 0.2
Rv1258c 1406691 p.Arg217Leu missense_variant 0.2
Rv1258c 1406744 c.597G>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471775 n.-71G>T upstream_gene_variant 0.22
rrl 1474086 n.429A>T non_coding_transcript_exon_variant 0.25
rrl 1475441 n.1785dupC non_coding_transcript_exon_variant 0.2
rrl 1475471 n.1814C>A non_coding_transcript_exon_variant 0.15
rrl 1476176 n.2519C>A non_coding_transcript_exon_variant 0.33
inhA 1673469 c.-733A>G upstream_gene_variant 0.17
inhA 1674332 p.Leu44Pro missense_variant 0.11
rpsA 1833987 p.Pro149His missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102178 p.Leu289Ile missense_variant 0.15
katG 2154586 p.Asp509Ala missense_variant 0.25
katG 2155218 p.Leu298Phe missense_variant 0.22
PPE35 2170100 c.513G>T synonymous_variant 0.29
PPE35 2170699 c.-87C>T upstream_gene_variant 0.13
Rv1979c 2222096 p.Ala357Ser missense_variant 0.25
Rv1979c 2222967 c.198G>T synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518066 c.-48delC upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714956 p.Tyr126Cys missense_variant 0.22
ahpC 2726621 p.Glu143Asp missense_variant 0.33
folC 2746802 p.Leu266Gln missense_variant 0.25
Rv2752c 3064597 p.Gly532Val missense_variant 0.14
thyX 3067342 p.Glu202* stop_gained 0.2
thyX 3067919 c.27G>T synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087287 c.468C>A synonymous_variant 0.22
Rv3083 3448317 c.-187G>T upstream_gene_variant 0.22
fprA 3473831 c.-176G>T upstream_gene_variant 0.17
fprA 3473976 c.-31C>T upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612497 p.Gly207Asp missense_variant 0.17
fbiB 3641937 p.Gly135Trp missense_variant 0.18
fbiB 3642772 p.Asp413Ala missense_variant 0.5
alr 3840323 c.1098C>T synonymous_variant 0.22
alr 3841060 p.Gly121Trp missense_variant 0.29
rpoA 3878144 c.363delC frameshift_variant 0.29
embC 4242299 p.Gly813Trp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246317 p.Pro1029Thr missense_variant 0.15
embB 4247323 c.810G>T synonymous_variant 0.25
embB 4247483 p.Gly324Cys missense_variant 0.18
embB 4248322 c.1809G>A synonymous_variant 0.22
aftB 4267164 p.Trp558Leu missense_variant 0.2
ethA 4328160 c.-687C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408029 c.174C>A synonymous_variant 0.17