TB-Profiler result

Run: SRR4035766
Summary

Run ID: SRR4035766

Sample name:

Date: 04-04-2023 07:17:09

Number of reads: 1102866

Percentage reads mapped: 99.53

Strain: lineage4.1.2

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 1.0
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
katG 2153928 p.Trp728Cys missense_variant 0.22 isoniazid
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 8061 p.Arg254Cys missense_variant 1.0
gyrA 8820 p.Asp507Asn missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576220 c.873C>T synonymous_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760241 c.435G>C synonymous_variant 0.12
rpoB 760250 p.Met148Ile missense_variant 0.13
rpoB 760360 p.Ile185Thr missense_variant 0.15
rpoB 760614 p.Asp270Asn missense_variant 0.14
rpoB 760638 p.Gly278Arg missense_variant 0.18
rpoB 762161 c.2355C>T synonymous_variant 0.22
rpoB 762313 p.Gly836Asp missense_variant 0.33
rpoC 762491 c.-879T>C upstream_gene_variant 0.11
rpoB 763162 p.Leu1119His missense_variant 0.25
rpoC 763362 c.-8G>T upstream_gene_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765446 p.Gln693Glu missense_variant 0.13
rpoC 765457 c.2088C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776335 p.Val716Met missense_variant 0.13
mmpL5 776808 p.Thr558Met missense_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpR5 778067 c.-923G>A upstream_gene_variant 0.13
mmpL5 778091 p.Trp130Cys missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801430 p.Val208Leu missense_variant 0.11
atpE 1461172 p.Pro43His missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472066 n.221T>C non_coding_transcript_exon_variant 0.25
rrs 1472971 n.1126G>T non_coding_transcript_exon_variant 0.2
rrl 1476020 n.2363A>T non_coding_transcript_exon_variant 0.4
fabG1 1673675 c.239delG frameshift_variant 0.14
rpsA 1834798 c.1257C>A synonymous_variant 0.13
tlyA 1917784 c.-156C>G upstream_gene_variant 0.12
tlyA 1917958 p.Val7Leu missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917977 p.Arg13Gln missense_variant 0.15
katG 2153902 p.Phe737Ser missense_variant 0.22
katG 2154036 c.2076C>T synonymous_variant 0.2
katG 2154286 p.Met609Lys missense_variant 0.17
katG 2156187 c.-76G>A upstream_gene_variant 0.2
katG 2156194 c.-83A>T upstream_gene_variant 0.18
katG 2156337 c.-226G>A upstream_gene_variant 0.22
PPE35 2167875 p.Gly913Asp missense_variant 0.13
PPE35 2168952 p.Asn554Ser missense_variant 0.17
PPE35 2169379 c.1233delG frameshift_variant 0.2
PPE35 2169535 p.Gly360Arg missense_variant 0.17
Rv1979c 2221730 p.Ser479Cys missense_variant 0.12
Rv1979c 2221859 p.Cys436Arg missense_variant 0.12
Rv1979c 2223085 p.Ile27Thr missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518221 p.Leu36Pro missense_variant 0.12
kasA 2518787 p.Arg225Trp missense_variant 0.13
ahpC 2726022 c.-171C>T upstream_gene_variant 0.17
folC 2747167 p.Lys144Asn missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449284 p.Trp261Arg missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568495 p.Pro62Leu missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612162 p.Ala319Pro missense_variant 0.12
fbiB 3641799 p.Lys89Glu missense_variant 0.11
fbiB 3642035 c.501T>A synonymous_variant 0.14
embC 4240457 p.Gly199Trp missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243424 c.196delG frameshift_variant 0.12
embA 4244840 c.1608G>C synonymous_variant 0.1
embA 4245010 p.Ala593Val missense_variant 0.14
embB 4247176 c.663G>T synonymous_variant 0.14
aftB 4266999 p.Cys613Ser missense_variant 0.12
aftB 4267016 c.1821C>T synonymous_variant 0.15
aftB 4267019 c.1818G>A synonymous_variant 0.17
aftB 4267030 p.Asp603His missense_variant 0.2
aftB 4267233 p.Asp535Gly missense_variant 0.12
aftB 4267395 p.Lys481Ile missense_variant 0.2
aftB 4267407 p.Lys477Met missense_variant 0.2
aftB 4267499 c.1338G>A synonymous_variant 0.14
ubiA 4269977 c.-144C>T upstream_gene_variant 0.12
ethA 4326207 p.Gly423Arg missense_variant 0.11
ethR 4327354 c.-195G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407987 c.216C>A synonymous_variant 0.17