TB-Profiler result

Run: ERR400381
Summary

Run ID: ERR400381

Sample name:

Date: 01-04-2023 03:45:36

Number of reads: 842240

Percentage reads mapped: 99.28

Strain: lineage1.1.3.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 Indo-Oceanic NA 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
gid 4407908 p.Glu99* stop_gained 0.12 streptomycin
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 6241 c.1002C>T synonymous_variant 0.13
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
fgd1 491447 p.Val222Ala missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575258 c.-90G>A upstream_gene_variant 0.13
mshA 575627 p.Ala94Ser missense_variant 0.15
mshA 575981 p.Arg212Trp missense_variant 0.12
mshA 576758 p.His471Tyr missense_variant 0.14
rpoB 761610 p.Gly602Trp missense_variant 0.18
rpoB 762832 p.Ser1009Ile missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777983 c.498G>C synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800690 c.-119C>A upstream_gene_variant 0.12
fbiC 1302844 c.-87C>A upstream_gene_variant 0.14
fbiC 1303676 p.Gly249Asp missense_variant 0.15
fbiC 1303759 p.Ile277Val missense_variant 0.12
fbiC 1303762 p.Arg278Ser missense_variant 0.12
Rv1258c 1407535 c.-195G>T upstream_gene_variant 0.12
embR 1416662 p.Arg229His missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103232 c.-190G>A upstream_gene_variant 0.91
katG 2154724 p.Arg463Leu 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
pncA 2290197 c.-957dupC upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518346 c.232C>A synonymous_variant 0.13
eis 2714561 p.Gly258Cys missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.19
ahpC 2726338 p.Val49Gly missense_variant 0.25
ahpC 2726341 p.Val50Gly missense_variant 0.25
pepQ 2859747 c.672C>A synonymous_variant 0.13
pepQ 2860110 c.309G>T synonymous_variant 0.13
ribD 2986963 p.Arg42Leu missense_variant 0.12
ribD 2987163 c.325C>A synonymous_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065309 p.Met295Leu missense_variant 0.12
thyX 3067431 p.Arg172Leu missense_variant 0.12
thyX 3067435 p.Ala171Ser missense_variant 1.0
thyA 3074508 c.-37C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087911 c.1092C>A synonymous_variant 0.14
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448998 c.495C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474031 p.Val9Met missense_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474878 p.Arg291His missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 0.95
fprA 3475348 p.Ala448Pro missense_variant 0.15
Rv3236c 3612669 p.Ala150Thr missense_variant 0.18
Rv3236c 3613299 c.-183C>T upstream_gene_variant 0.13
fbiB 3641148 c.-387C>T upstream_gene_variant 1.0
fbiA 3641509 p.Gly323Trp missense_variant 0.14
fbiB 3641628 p.Ala32Ser missense_variant 0.13
fbiB 3641794 p.Ala87Val missense_variant 0.17
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4039717 p.Lys330Glu missense_variant 0.11
clpC1 4039765 p.Arg314Cys missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240655 p.Ala265Pro missense_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241085 p.Leu408Pro missense_variant 0.1
embC 4241241 p.Leu460Arg missense_variant 1.0
embA 4242554 c.-679T>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243499 c.267G>A synonymous_variant 0.14
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244677 p.Ser482* stop_gained 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246689 p.Pro59Leu missense_variant 0.12
embB 4246786 p.Met91Ile missense_variant 0.94
embB 4246820 p.Pro103Ala missense_variant 0.15
embB 4247158 c.645C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247681 p.Val390Phe missense_variant 0.12
embB 4247707 c.1194C>T synonymous_variant 1.0
embB 4247774 p.Arg421Trp missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269999 c.-166G>T upstream_gene_variant 0.18
ethA 4328397 c.-924G>A upstream_gene_variant 0.12
gid 4407583 p.Arg207His missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0