TB-Profiler result

Run: SRR6855862
Summary

Run ID: SRR6855862

Sample name:

Date: 04-04-2023 17:48:07

Number of reads: 436427

Percentage reads mapped: 99.3

Strain: lineage1.2.2.1

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_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
fgd1 491060 p.Met93Thr missense_variant 1.0
fgd1 491542 c.760T>C synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575381 c.34T>C synonymous_variant 0.12
mshA 576603 p.Arg419Leu missense_variant 0.17
mshA 576746 p.Gly467Arg missense_variant 1.0
ccsA 620659 p.Arg257Cys missense_variant 1.0
rpoB 760301 c.495C>T synonymous_variant 1.0
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 764502 p.Val378Ala missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778644 p.Trp88Arg missense_variant 0.14
mmpR5 779194 p.Thr69Ala missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 1.0
fbiC 1305310 p.Arg794Trp missense_variant 0.11
Rv1258c 1406775 p.Ala189Val missense_variant 0.17
Rv1258c 1407502 c.-162G>A upstream_gene_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrl 1474180 n.523T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102351 p.Arg231Gln missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168815 p.Thr600Ala missense_variant 0.11
PPE35 2169601 p.Asn338Asp missense_variant 0.12
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
folC 2746740 p.Ser287Pro missense_variant 0.17
pepQ 2859364 p.Pro352Leu missense_variant 0.17
pepQ 2859657 c.762C>T synonymous_variant 0.17
ribD 2987152 p.His105Arg missense_variant 0.12
thyX 3068115 c.-170C>T upstream_gene_variant 1.0
thyA 3074034 c.438T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087632 p.Gln271His missense_variant 0.17
fbiD 3339741 c.624G>T synonymous_variant 0.25
fbiD 3339744 c.627A>C synonymous_variant 0.22
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448719 c.216G>A synonymous_variant 1.0
Rv3083 3449074 p.Thr191Ala missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474273 c.267G>A synonymous_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474679 p.Ile225Val missense_variant 1.0
fprA 3474952 p.Gln316* stop_gained 0.15
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640763 c.226delC frameshift_variant 0.13
fbiB 3642820 p.Ala429Val missense_variant 0.12
alr 3840515 c.906A>G synonymous_variant 0.1
alr 3840898 c.522delC frameshift_variant 0.14
rpoA 3878349 p.Ser53Arg missense_variant 0.14
clpC1 4038844 p.Val621Leu missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245834 c.2603_2609delTGGTGGT frameshift_variant 0.67
embA 4245844 p.Val871Glu missense_variant 0.5
embA 4245846 p.Ser872Thr missense_variant 0.67
embA 4245848 c.2616_2617insACCACCA frameshift_variant 0.67
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246809 p.Leu99Arg missense_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248390 c.1879delG frameshift_variant 0.11
embB 4248950 p.Tyr813His missense_variant 0.12
aftB 4267376 c.1461T>C synonymous_variant 0.12
aftB 4268672 c.165C>T synonymous_variant 0.25
aftB 4268852 c.-16G>A upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326687 p.Met263Val missense_variant 1.0
ethR 4327450 c.-99G>A upstream_gene_variant 1.0
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 4407873 c.330G>T synonymous_variant 1.0
gid 4408027 p.Leu59Pro missense_variant 0.11