TB-Profiler result

Run: SRR14088376
Summary

Run ID: SRR14088376

Sample name:

Date: 03-04-2023 09:46:20

Number of reads: 755461

Percentage reads mapped: 99.5

Strain: lineage3

Drug-resistance: MDR-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 761128 p.Ser441Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 5625 c.387delC frameshift_variant 0.12
gyrB 6737 p.Thr500Ala missense_variant 1.0
gyrA 6844 c.-458T>C upstream_gene_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7958 c.657C>T synonymous_variant 1.0
gyrA 8282 c.981G>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490908 c.126G>A synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619814 c.-77G>T upstream_gene_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.31
rpoB 759615 c.-192A>C upstream_gene_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760300 p.Thr165Asn missense_variant 0.22
rpoB 760461 p.Arg219Cys missense_variant 0.22
rpoB 760659 p.Ser285Thr missense_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775812 p.Phe890Ala missense_variant 0.11
mmpL5 775817 c.2664T>C synonymous_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776265 p.Lys739Arg missense_variant 1.0
mmpL5 778011 p.Gln157Arg missense_variant 0.12
mmpR5 779186 p.Gly66Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800888 p.Thr27Asn missense_variant 0.17
embR 1417457 c.-110C>T upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673606 p.Phe56Ser missense_variant 0.1
rpsA 1833515 c.-27C>A upstream_gene_variant 0.12
rpsA 1833909 p.Asp123Gly missense_variant 0.33
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101700 p.Leu448Gln missense_variant 0.13
ndh 2101702 c.1341G>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156259 c.-148T>C upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168975 c.1638C>G synonymous_variant 0.5
PPE35 2169044 c.1569G>C synonymous_variant 1.0
PPE35 2169047 p.Ile522Val missense_variant 1.0
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.82
PPE35 2170053 p.Thr187Ser missense_variant 0.82
PPE35 2170627 c.-15G>A upstream_gene_variant 1.0
Rv1979c 2222042 p.Thr375Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289018 c.218_223delTCAGCG disruptive_inframe_deletion 0.17
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518154 p.Val14Leu missense_variant 0.15
kasA 2518158 p.Val15Glu missense_variant 0.17
eis 2714566 p.Leu256Pro missense_variant 0.15
eis 2715050 p.Gly95Arg missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986748 c.-91A>G upstream_gene_variant 0.11
ribD 2987440 p.Thr201Ile missense_variant 0.33
Rv2752c 3065722 p.Ala157Val missense_variant 0.22
Rv2752c 3065983 p.Arg70Gln missense_variant 0.17
thyA 3074401 p.Thr24Ile missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448441 c.-63A>G upstream_gene_variant 0.22
Rv3083 3449217 p.Trp238* stop_gained 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474887 p.Leu294Pro missense_variant 0.11
whiB7 3568473 p.Glu69Asp missense_variant 0.2
fbiB 3640584 c.-951C>A upstream_gene_variant 0.4
alr 3840497 c.924G>A synonymous_variant 0.12
panD 4044203 p.Thr27Pro missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244900 c.1668G>A synonymous_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246548 p.Pro12Gln missense_variant 0.68
embB 4246555 c.42G>C synonymous_variant 0.76
embB 4246556 p.Ala15Pro missense_variant 0.76
embB 4246563 p.Leu17Trp missense_variant 0.58
embB 4246567 c.54G>T synonymous_variant 0.48
embB 4249783 c.3270A>G synonymous_variant 0.12
ethA 4326079 c.1395C>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407732 c.463_470delCCGAACGG frameshift_variant 1.0