TB-Profiler result

Run: SRR4033472

Summary

Run ID: SRR4033472

Sample name:

Date: 04-04-2023 06:07:08

Number of reads: 1341834

Percentage reads mapped: 99.61

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
katG 2153955 c.2156delA frameshift_variant 0.13 isoniazid
ethA 4326608 c.864_865delCT frameshift_variant 0.12 ethionamide
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>C upstream_gene_variant 0.12
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6320 p.Lys361Glu missense_variant 0.13
gyrB 7063 p.Gln608His missense_variant 0.12
gyrB 7155 p.Asp639Gly missense_variant 0.15
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7613 c.312G>T synonymous_variant 0.13
gyrA 8281 p.Val327Ala missense_variant 0.1
gyrA 8533 p.Ser411Leu missense_variant 0.22
gyrA 8881 p.Lys527Met missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9508 p.Ala736Val missense_variant 0.15
gyrA 9522 p.Pro741Ala missense_variant 0.13
fgd1 490957 p.Thr59Ala missense_variant 0.12
ccsA 619711 c.-180G>A upstream_gene_variant 0.12
ccsA 619746 c.-145A>T upstream_gene_variant 0.17
rpoB 760941 p.Ile379Phe missense_variant 0.15
rpoB 761012 c.1206C>T synonymous_variant 0.12
rpoB 761709 p.Val635Ile missense_variant 0.3
rpoB 761755 p.Asp650Gly missense_variant 0.12
rpoB 763138 p.Ile1111Thr missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775770 p.Ala904Gly missense_variant 0.12
mmpL5 776746 p.Arg579Ser missense_variant 0.22
mmpL5 777322 p.Val387Ile missense_variant 0.17
mmpL5 777502 p.Thr327Ala missense_variant 0.12
mmpL5 777524 c.957T>A synonymous_variant 0.15
mmpL5 777810 p.Arg224Gln missense_variant 0.15
mmpL5 777818 c.663G>T synonymous_variant 0.14
mmpL5 778304 p.Ile59Met missense_variant 0.11
mmpL5 779304 c.-824A>G upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304897 p.Leu656Pro missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471830 n.-16A>G upstream_gene_variant 0.12
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474665 n.1008A>T non_coding_transcript_exon_variant 0.14
rrl 1475059 n.1402G>T non_coding_transcript_exon_variant 0.25
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17
rrl 1475789 n.2132C>A non_coding_transcript_exon_variant 0.13
inhA 1674501 p.Gln100His missense_variant 0.14
rpsA 1833548 p.Ser3Gly missense_variant 0.12
rpsA 1834118 p.Gln193* stop_gained 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103199 c.-157G>A upstream_gene_variant 0.14
ndh 2103207 c.-165C>T upstream_gene_variant 0.14
ndh 2103241 c.-199T>G upstream_gene_variant 0.12
katG 2154663 c.1449C>T synonymous_variant 0.14
katG 2156139 c.-28G>A upstream_gene_variant 0.13
katG 2156189 c.-78C>A upstream_gene_variant 0.18
katG 2156334 c.-223G>A upstream_gene_variant 0.13
Rv1979c 2222413 p.Asn251Ile missense_variant 0.14
Rv1979c 2222893 p.Gly91Asp missense_variant 0.15
Rv1979c 2223095 p.Ile24Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289398 c.-157G>A upstream_gene_variant 0.13
kasA 2518073 c.-42T>A upstream_gene_variant 0.13
folC 2747540 c.58delA frameshift_variant 0.12
Rv2752c 3065383 c.808delA frameshift_variant 0.13
thyX 3067615 p.Glu111* stop_gained 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087302 p.Gly162Trp missense_variant 0.21
ald 3087720 p.Met301Val missense_variant 0.11
fbiD 3339575 p.Ala153Val missense_variant 0.13
Rv3083 3448951 c.448C>T synonymous_variant 0.15
Rv3083 3449327 p.Arg275His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612022 c.1095C>A synonymous_variant 0.15
Rv3236c 3612034 c.1083C>G synonymous_variant 0.18
fbiA 3640901 p.Gln120Arg missense_variant 0.17
alr 3840574 p.Leu283Met missense_variant 0.15
ddn 3987183 p.Ala114Thr missense_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039947 p.Gly253Val missense_variant 0.15
clpC1 4040415 p.Gln97Arg missense_variant 0.13
panD 4044099 c.183C>T synonymous_variant 0.15
embC 4240316 p.Cys152Arg missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242968 p.Thr1036Ala missense_variant 0.11
embA 4243953 p.Arg241Cys missense_variant 0.13
embA 4243989 p.Ala253Thr missense_variant 0.15
embB 4247241 p.Asp243Gly missense_variant 0.11
aftB 4267204 p.Lys545Glu missense_variant 0.11
aftB 4268081 p.Gln252His missense_variant 0.18
ethA 4327407 p.Leu23Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407863 p.Ile114Val missense_variant 0.18
gid 4408156 p.Leu16Arg missense_variant 1.0