TB-Profiler result

Run: SRR4035542

Summary

Run ID: SRR4035542

Sample name:

Date: 04-04-2023 07:09:56

Number of reads: 1070286

Percentage reads mapped: 99.49

Strain: lineage3

Drug-resistance: RR-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
lineage3 East-African-Indian CAS RD750 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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575351 p.Ala2Ser missense_variant 0.15
mshA 575366 p.Asp7Asn missense_variant 0.2
mshA 576611 p.Ala422Thr missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 0.95
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766171 c.2802C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800751 c.-58C>T upstream_gene_variant 0.13
atpE 1461137 c.93C>T synonymous_variant 0.15
atpE 1461164 c.120C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833808 c.269_270dupTG frameshift_variant 0.11
rpsA 1834964 c.1428delA frameshift_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155706 p.Pro136Ser missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.2
Rv1979c 2223261 c.-97A>T upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714721 c.612C>T synonymous_variant 0.24
eis 2714767 p.Gly189Val missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067525 p.Ala141Thr missense_variant 0.33
thyX 3068010 c.-65C>T upstream_gene_variant 0.13
thyA 3073806 c.666C>G synonymous_variant 0.14
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339688 p.Thr191Pro missense_variant 0.31
Rv3083 3448979 p.Phe159Ser missense_variant 0.11
Rv3083 3449166 c.663G>A synonymous_variant 0.18
Rv3083 3449375 c.873delG frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.14
alr 3841148 c.273C>T synonymous_variant 0.12
rpoA 3878393 p.Arg39Cys missense_variant 0.19
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268069 c.768C>T synonymous_variant 0.13
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0