TB-Profiler result

Run: SRR6797701
Summary

Run ID: SRR6797701

Sample name:

Date: 04-04-2023 16:15:56

Number of reads: 1095730

Percentage reads mapped: 98.76

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9499 p.Lys733Arg missense_variant 0.12
fgd1 491018 p.Phe79Ser missense_variant 0.38
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575661 p.Pro105His missense_variant 0.15
rpoB 759974 p.Glu56Asp missense_variant 0.14
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761865 p.Gly687Cys missense_variant 0.13
rpoB 761885 c.2079T>A synonymous_variant 0.14
rpoB 762321 p.Gly839Cys missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775652 c.2829C>A synonymous_variant 0.14
mmpL5 776095 p.Arg796Cys missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801024 c.216C>A synonymous_variant 0.15
Rv1258c 1406691 p.Arg217Leu missense_variant 0.22
Rv1258c 1406885 c.456G>A synonymous_variant 1.0
Rv1258c 1407347 c.-7G>T upstream_gene_variant 0.14
embR 1416628 c.720C>T synonymous_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417542 c.-195C>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673987 p.Pro183Gln missense_variant 0.17
fabG1 1674174 p.Met245Ile missense_variant 0.12
fabG1 1674179 p.His247Leu missense_variant 0.12
inhA 1674957 c.756G>T synonymous_variant 0.13
rpsA 1833910 p.Asp123Glu missense_variant 0.15
rpsA 1833970 c.429G>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918208 p.Gly90Asp missense_variant 0.22
ndh 2101955 p.Gln363Ser missense_variant 1.0
katG 2154663 p.Phe483Leu missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156570 c.-459C>A upstream_gene_variant 0.33
PPE35 2167701 p.Ala971Gly missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.22
folC 2747117 p.Ala161Val missense_variant 0.25
pepQ 2860518 c.-100C>A upstream_gene_variant 0.11
ribD 2987347 p.Pro170Gln missense_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>C upstream_gene_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473904 c.-103T>A upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474365 p.Pro120Gln missense_variant 0.22
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612783 p.Gly112Trp missense_variant 0.15
Rv3236c 3613007 p.Leu37Ser missense_variant 0.14
fbiA 3640774 p.Gly78Cys missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044234 c.48C>A synonymous_variant 0.18
embC 4240075 p.Glu71Asp missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242542 p.Arg894Cys missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245218 c.1986C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247548 c.1035C>T synonymous_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268340 p.Pro166Gln missense_variant 0.18
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326522 p.Glu318* stop_gained 0.12
ethA 4326990 p.Ile162Phe missense_variant 0.15
ethA 4327297 p.Met59Ile missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407688 p.Arg172Leu missense_variant 0.15
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408157 p.Leu16Ile missense_variant 0.22
gid 4408161 c.42G>A synonymous_variant 0.22