TB-Profiler result

Run: SRR4036025

Summary

Run ID: SRR4036025

Sample name:

Date: 04-04-2023 07:27:10

Number of reads: 1151622

Percentage reads mapped: 99.47

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 0.99
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 761095 p.Leu430Pro missense_variant 0.11 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
ahpC 2726142 c.-51G>T upstream_gene_variant 0.14 isoniazid
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 5590 c.351T>A synonymous_variant 0.17
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 8875 p.Tyr525Cys missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9400 p.Val700Ala missense_variant 0.25
gyrA 9477 p.Ala726Thr missense_variant 0.33
gyrA 9708 c.2407T>C synonymous_variant 0.12
gyrA 9792 p.Asn831Tyr missense_variant 0.17
fgd1 490701 c.-82A>G upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575264 c.-84C>A upstream_gene_variant 0.15
mshA 575285 c.-63G>C upstream_gene_variant 0.12
mshA 575397 p.Arg17His missense_variant 0.18
mshA 575678 p.Asn111Asp missense_variant 0.12
mshA 575799 p.Val151Ala missense_variant 0.11
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761191 p.Ala462Gly missense_variant 0.12
rpoB 761401 p.Arg532His missense_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763115 c.-255T>C upstream_gene_variant 0.11
rpoC 764745 p.Arg459Gln missense_variant 0.15
rpoC 764778 p.Lys470Thr missense_variant 0.14
rpoC 764834 p.Glu489Lys missense_variant 0.14
rpoC 764842 p.Ile491Met missense_variant 0.14
rpoC 764918 p.Val517Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776271 p.Lys737Met missense_variant 0.17
mmpL5 777036 p.Gln482Arg missense_variant 0.17
mmpL5 777145 p.Glu446Lys missense_variant 0.2
mmpL5 777226 p.Asn419Asp missense_variant 0.2
rpsL 781392 c.-168C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781781 c.222G>A synonymous_variant 0.15
rpsL 781784 p.Gln75His missense_variant 0.13
rplC 800896 p.Lys30Glu missense_variant 0.12
fbiC 1304365 p.Gln479* stop_gained 0.17
fbiC 1304411 p.Asp494Gly missense_variant 0.11
fbiC 1304431 p.Ser501Pro missense_variant 0.1
fbiC 1304783 p.Val618Asp missense_variant 0.12
fbiC 1304868 c.1938G>A synonymous_variant 0.15
Rv1258c 1407339 c.2T>A start_lost 0.14
embR 1416224 p.Glu375Ala missense_variant 0.1
embR 1416790 c.558G>A synonymous_variant 0.17
embR 1416927 p.Ala141Thr missense_variant 0.2
embR 1417077 p.Arg91Trp missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472117 n.272A>T non_coding_transcript_exon_variant 0.15
rrl 1473909 n.252G>T non_coding_transcript_exon_variant 0.14
rrl 1475901 n.2244C>G non_coding_transcript_exon_variant 0.22
rrl 1476708 n.3051C>A non_coding_transcript_exon_variant 0.15
inhA 1674605 p.Leu135Pro missense_variant 0.11
rpsA 1833373 c.-169G>A upstream_gene_variant 0.17
rpsA 1833426 c.-116T>C upstream_gene_variant 0.17
rpsA 1834139 p.Ser200Cys missense_variant 0.13
rpsA 1834264 c.723G>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102414 p.Arg210Gln missense_variant 0.14
ndh 2102421 c.621dupC frameshift_variant 0.14
ndh 2102471 p.Glu191Ala missense_variant 0.15
ndh 2102489 p.Met185Lys missense_variant 0.17
ndh 2102502 p.Thr181Ala missense_variant 0.13
katG 2154007 p.Ser702Leu missense_variant 0.2
katG 2154134 p.Asn660Asp missense_variant 0.14
katG 2154339 c.1773A>G synonymous_variant 0.14
katG 2154368 p.Glu582Lys missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154937 p.Arg392Gln missense_variant 0.15
katG 2155056 c.1056A>G synonymous_variant 0.2
katG 2156134 c.-23C>A upstream_gene_variant 0.12
katG 2156440 c.-329A>G upstream_gene_variant 0.12
PPE35 2167881 p.Asn911Ser missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168034 p.Thr860Ile missense_variant 0.12
PPE35 2168143 p.Phe824Val missense_variant 0.15
PPE35 2168168 p.Met815Ile missense_variant 0.14
PPE35 2168176 p.Gln813* stop_gained 0.13
PPE35 2168353 p.Ile754Val missense_variant 0.11
PPE35 2168410 p.Thr735Ala missense_variant 0.11
PPE35 2169459 p.Gly385Asp missense_variant 0.13
PPE35 2170254 p.Leu120Pro missense_variant 0.11
Rv1979c 2221750 p.Arg472Leu missense_variant 0.17
Rv1979c 2222625 c.540C>T synonymous_variant 0.25
Rv1979c 2223025 p.Ala47Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223333 c.-169G>C upstream_gene_variant 0.14
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289845 c.-604G>A upstream_gene_variant 0.14
pncA 2290018 c.-777C>T upstream_gene_variant 0.2
kasA 2518228 c.114C>G synonymous_variant 0.13
kasA 2519048 p.Gly312Ser missense_variant 0.13
eis 2714419 p.Leu305His missense_variant 0.33
eis 2714707 p.Gly209Asp missense_variant 0.14
eis 2714712 c.621G>C synonymous_variant 0.14
eis 2715131 p.Arg68Trp missense_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747692 c.-94A>G upstream_gene_variant 0.14
pepQ 2859488 p.Thr311Ala missense_variant 0.12
pepQ 2859775 p.Gly215Asp missense_variant 0.15
ribD 2986681 c.-158A>T upstream_gene_variant 0.13
ribD 2986693 c.-146C>T upstream_gene_variant 0.13
ribD 2986695 c.-144A>G upstream_gene_variant 0.14
Rv2752c 3064775 p.Val473Ile missense_variant 0.13
Rv2752c 3065379 c.813C>T synonymous_variant 0.2
Rv2752c 3067025 c.-834G>C upstream_gene_variant 0.17
Rv2752c 3067128 c.-938delG upstream_gene_variant 0.13
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087187 p.Ala123Val missense_variant 0.12
fbiD 3338967 c.-151C>T upstream_gene_variant 0.13
fbiD 3339350 p.Asp78Gly missense_variant 0.11
Rv3083 3448730 p.Ala76Val missense_variant 0.13
Rv3083 3449942 p.Asp480Gly missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474465 p.Ile153Met missense_variant 0.11
fprA 3474663 c.661delG frameshift_variant 0.22
whiB7 3568692 c.-14delA upstream_gene_variant 0.14
whiB7 3568705 c.-26A>G upstream_gene_variant 0.12
Rv3236c 3612561 p.Thr186Ser missense_variant 0.15
Rv3236c 3612732 c.384delC frameshift_variant 0.13
fbiA 3640973 p.Pro144Arg missense_variant 0.12
fbiA 3641525 p.Gly328Glu missense_variant 0.12
fbiB 3641957 c.423C>G synonymous_variant 0.15
fbiB 3642489 p.Ser319Pro missense_variant 0.17
alr 3840825 p.Tyr199Cys missense_variant 0.1
rpoA 3877513 p.Thr332Ile missense_variant 0.13
rpoA 3878324 p.Glu62Lys missense_variant 0.2
rpoA 3878378 p.Ser44Thr missense_variant 0.13
clpC1 4038494 c.2211G>C synonymous_variant 0.13
clpC1 4039860 p.Ile282Asn missense_variant 0.12
clpC1 4040073 p.Asn211Ser missense_variant 0.12
embC 4239734 c.-129C>A upstream_gene_variant 0.22
embC 4240702 c.840G>A synonymous_variant 0.13
embC 4241997 p.Thr712Met missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242310 c.-923C>A upstream_gene_variant 0.18
embA 4242316 c.-917C>T upstream_gene_variant 0.29
embC 4242320 p.Pro820Ala missense_variant 0.25
embA 4242586 c.-647C>A upstream_gene_variant 0.33
embC 4242606 p.Met915Lys missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242687 p.Gln942Arg missense_variant 0.18
embA 4242877 c.-356G>A upstream_gene_variant 0.18
embC 4242920 p.Ala1020Thr missense_variant 0.14
embC 4242933 p.Val1024Ala missense_variant 0.14
embC 4242951 p.Gly1030Val missense_variant 0.14
embC 4242963 p.Gly1034Asp missense_variant 0.17
embC 4242999 p.Ala1046Val missense_variant 0.25
embA 4245337 p.Val702Gly missense_variant 0.12
embA 4246056 p.Val942Ile missense_variant 0.13
embB 4246999 c.486C>G synonymous_variant 0.22
embB 4247284 c.771G>A synonymous_variant 0.14
embB 4247485 c.972C>T synonymous_variant 0.14
embB 4247498 p.Pro329Ser missense_variant 0.15
embB 4248638 p.Ile709Phe missense_variant 0.25
aftB 4267013 c.1824T>C synonymous_variant 0.18
aftB 4267472 c.1364delG frameshift_variant 0.15
aftB 4268113 p.Ala242Pro missense_variant 0.14
aftB 4268126 c.711G>A synonymous_variant 0.12
aftB 4268174 c.663G>T synonymous_variant 0.14
aftB 4268608 p.Met77Val missense_variant 0.12
aftB 4269249 c.-413G>A upstream_gene_variant 0.15
ethA 4326326 p.Thr383Met missense_variant 0.13
ethA 4326580 p.Asn298Lys missense_variant 0.14
ethR 4327884 p.Glu112Asp missense_variant 0.11
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338264 c.258G>C synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338602 c.-81A>T upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0