TB-Profiler result

Run: ERR9891970
Summary

Run ID: ERR9891970

Sample name:

Date: 02-04-2023 13:25:35

Number of reads: 686708

Percentage reads mapped: 98.77

Strain: lineage3

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
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
gid 4407851 c.351delG 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.97
gyrA 9428 p.Asp709Glu missense_variant 0.1
fgd1 490926 c.144C>A synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576459 c.1117_1147delGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCG frameshift_variant 0.18
ccsA 619831 c.-60T>G upstream_gene_variant 0.4
ccsA 619848 c.-43C>A upstream_gene_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766582 c.3213C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 777180 p.Ala434Glu missense_variant 0.12
mmpS5 778757 p.Pro50Leu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.26
embR 1417442 c.-95C>A upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674451 p.Ala84Ser missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918257 c.318C>G synonymous_variant 0.11
ndh 2103225 c.-183A>C upstream_gene_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
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
kasA 2519115 p.Ala334Val missense_variant 0.14
eis 2714872 p.Pro154Gln missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987239 p.Thr134Ile missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448755 c.252C>T synonymous_variant 1.0
Rv3083 3449072 p.Val190Gly missense_variant 0.22
fprA 3473935 c.-72C>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612446 p.Gly224Val missense_variant 0.13
fbiA 3640856 p.Gly105Val missense_variant 0.12
fbiB 3641115 c.-420A>G upstream_gene_variant 0.11
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4039363 p.Ala448Thr missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248422 p.Ala637Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0