TB-Profiler result

Run: SRR4035752
Summary

Run ID: SRR4035752

Sample name:

Date: 04-04-2023 07:16:42

Number of reads: 1610910

Percentage reads mapped: 99.46

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 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 2154987 c.1124delC frameshift_variant 0.17 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
gyrB 5096 c.-144A>T upstream_gene_variant 0.15
gyrB 5700 p.Glu154Gly missense_variant 0.11
gyrB 7200 p.Glu654Gly missense_variant 0.12
gyrA 7252 c.-50G>A upstream_gene_variant 0.22
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 8364 p.Thr355Ala missense_variant 0.11
gyrA 8377 p.Asp359Gly missense_variant 0.12
gyrA 8390 c.1089C>T synonymous_variant 0.15
gyrA 9051 p.Leu584Met missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9736 p.Leu812Pro missense_variant 0.12
fgd1 491254 p.Lys158Glu missense_variant 0.15
fgd1 491327 p.Ala182Val missense_variant 0.18
fgd1 491485 p.Tyr235His missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575709 p.Asp121Val missense_variant 0.13
mshA 575768 p.Ala141Ser missense_variant 0.22
ccsA 620047 p.Ser53Pro missense_variant 0.11
ccsA 620336 p.Leu149Pro missense_variant 0.13
rpoB 760098 p.Ser98Thr missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762560 c.-810A>G upstream_gene_variant 0.11
rpoC 763333 c.-37G>A upstream_gene_variant 0.17
rpoC 763516 c.147G>A synonymous_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764587 c.1218C>T synonymous_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765643 c.2274G>A synonymous_variant 0.17
rpoC 766090 c.2721C>T synonymous_variant 0.13
rpoC 766360 c.2991C>T synonymous_variant 0.13
rpoC 766596 p.Val1076Ala missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776906 p.Gln525His missense_variant 0.1
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303637 p.Lys236Arg missense_variant 0.12
fbiC 1304068 p.Val380Ile missense_variant 0.15
fbiC 1304448 c.1518C>A synonymous_variant 0.16
Rv1258c 1406098 c.1242delC frameshift_variant 0.14
Rv1258c 1407108 p.Ala78Val missense_variant 0.15
Rv1258c 1407138 p.Tyr68Cys missense_variant 0.13
atpE 1461094 p.Met17Thr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472068 n.223T>A non_coding_transcript_exon_variant 0.25
rrs 1472210 n.367delT non_coding_transcript_exon_variant 0.14
rrs 1472728 n.883G>A non_coding_transcript_exon_variant 0.17
rrs 1472753 n.908A>T non_coding_transcript_exon_variant 0.22
rrs 1473017 n.1172A>T non_coding_transcript_exon_variant 0.18
rrl 1474044 n.387C>T non_coding_transcript_exon_variant 0.67
rrl 1474367 n.710T>A non_coding_transcript_exon_variant 0.22
rrl 1474398 n.741A>C non_coding_transcript_exon_variant 0.29
rrl 1474791 n.1134C>A non_coding_transcript_exon_variant 0.22
rrl 1474911 n.1254G>A non_coding_transcript_exon_variant 0.22
rrl 1475434 n.1777G>T non_coding_transcript_exon_variant 0.25
rrl 1476331 n.2674G>T non_coding_transcript_exon_variant 0.22
rrl 1476543 n.2886G>C non_coding_transcript_exon_variant 0.15
fabG1 1673822 p.Gln128Leu missense_variant 0.15
inhA 1673946 c.-256C>T upstream_gene_variant 0.13
inhA 1674714 c.513C>T synonymous_variant 0.15
rpsA 1833645 p.Asp35Val missense_variant 0.18
rpsA 1833656 p.Val39Ile missense_variant 0.22
rpsA 1833807 p.Leu89Pro missense_variant 0.11
rpsA 1834398 p.His286Leu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918535 p.His199Arg missense_variant 0.12
katG 2156329 c.-218C>T upstream_gene_variant 0.12
PPE35 2168025 p.Ala863Val missense_variant 0.14
PPE35 2168304 p.Thr770Met missense_variant 0.17
PPE35 2168480 c.2133C>T synonymous_variant 0.13
PPE35 2169291 p.Val441Asp missense_variant 0.18
PPE35 2170263 p.Leu117His missense_variant 0.15
Rv1979c 2222425 p.Ala247Glu missense_variant 0.15
Rv1979c 2223073 p.Gly31Asp missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518947 p.Val278Glu missense_variant 0.12
eis 2714434 p.Asn300Ser missense_variant 0.11
eis 2714491 p.Asp281Val missense_variant 0.14
ahpC 2725954 c.-239C>T upstream_gene_variant 0.13
pepQ 2859608 p.Arg271Trp missense_variant 0.15
pepQ 2860487 c.-69G>T upstream_gene_variant 0.14
ribD 2987385 p.Ala183Ser missense_variant 0.18
ribD 2987445 p.Val203Ile missense_variant 0.22
thyX 3067331 c.615C>T synonymous_variant 0.18
thyA 3073870 c.601delT frameshift_variant 0.15
thyA 3074480 c.-9G>A upstream_gene_variant 0.17
thyA 3074492 c.-21T>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087717 p.Asn300Asp missense_variant 0.12
ald 3087724 p.Pro302Arg missense_variant 0.11
ald 3087927 c.1108C>T synonymous_variant 0.12
Rv3083 3448979 p.Phe159Tyr missense_variant 0.14
Rv3083 3449115 c.612C>A synonymous_variant 0.14
Rv3083 3449125 p.Thr208Ala missense_variant 0.15
Rv3083 3449336 p.Gly278Asp missense_variant 0.2
Rv3083 3449896 p.His465Tyr missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiB 3640788 c.-747T>C upstream_gene_variant 0.14
fbiB 3642071 c.537C>G synonymous_variant 0.12
fbiB 3642391 p.Ala286Glu missense_variant 0.12
fbiB 3642395 c.861A>G synonymous_variant 0.13
fbiB 3642805 p.Ile424Thr missense_variant 0.14
alr 3840723 p.His233Leu missense_variant 0.14
rpoA 3878641 c.-134C>G upstream_gene_variant 0.27
ddn 3986959 p.Gly39Asp missense_variant 0.2
clpC1 4038855 p.Lys617Thr missense_variant 0.11
clpC1 4038884 c.1821C>A synonymous_variant 0.15
embC 4240012 c.152delC frameshift_variant 0.12
embC 4240726 c.864G>T synonymous_variant 0.2
embC 4240806 p.Arg315His missense_variant 0.25
embC 4241705 p.Ser615Pro missense_variant 0.12
embA 4242421 c.-812C>T upstream_gene_variant 0.15
embC 4242425 p.Arg855* stop_gained 0.15
embC 4242495 p.Asp878Gly missense_variant 0.13
embA 4242559 c.-674G>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244767 c.1539delG frameshift_variant 0.14
embA 4245434 c.2202G>A synonymous_variant 0.18
embB 4246913 p.Ser134Pro missense_variant 0.15
embB 4246942 c.429G>A synonymous_variant 0.14
embB 4246947 p.Cys145Tyr missense_variant 0.21
aftB 4267836 p.Met334Lys missense_variant 0.12
aftB 4268705 c.132C>G synonymous_variant 0.15
ethA 4327176 p.Phe100Leu missense_variant 0.11
ethR 4328072 p.Leu175Pro missense_variant 0.1
whiB6 4338525 c.-4G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0