TB-Profiler result

Run: SRR3732648
Summary

Run ID: SRR3732648

Sample name:

Date: 04-04-2023 05:37:01

Number of reads: 1194167

Percentage reads mapped: 99.4

Strain: lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
ethA 4326231 c.1242dupT frameshift_variant 0.14 ethionamide, ethionamide
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 7762 p.Pro154His missense_variant 0.15
gyrA 8567 c.1266C>A synonymous_variant 0.17
fgd1 491210 p.Trp143Leu missense_variant 0.12
fgd1 491492 p.Pro237His missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576205 c.858G>T synonymous_variant 0.5
mshA 576712 c.1365G>T synonymous_variant 0.4
ccsA 620528 p.Ala213Val missense_variant 0.22
ccsA 620835 c.945C>A synonymous_variant 0.25
rpoB 759757 c.-50G>A upstream_gene_variant 0.13
rpoB 759953 p.Asp49Glu missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761815 p.Ala670Asp missense_variant 0.15
rpoB 762138 p.Leu778Met missense_variant 0.18
rpoB 762532 p.Ile909Thr missense_variant 0.2
rpoC 762596 c.-774G>T upstream_gene_variant 0.17
rpoB 762682 p.Glu959Gly missense_variant 0.13
rpoC 764338 p.Glu323Asp missense_variant 0.25
rpoC 764785 c.1416C>A synonymous_variant 0.29
rpoC 765136 c.1767C>T synonymous_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766067 p.Glu900* stop_gained 0.12
rpoC 766356 p.Gly996Val missense_variant 0.4
rpoC 766690 c.3321G>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776393 c.2088C>T synonymous_variant 0.18
mmpL5 776561 c.1919delA frameshift_variant 0.2
mmpL5 776803 c.1677delG frameshift_variant 0.12
mmpL5 777908 c.573G>A synonymous_variant 0.18
mmpR5 778337 c.-653G>T upstream_gene_variant 0.18
mmpL5 778939 c.-459C>A upstream_gene_variant 0.14
mmpL5 779076 c.-596G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801406 p.Gly200Cys missense_variant 0.25
fbiC 1302897 c.-34G>T upstream_gene_variant 0.29
fbiC 1303977 c.1047C>A synonymous_variant 0.67
fbiC 1304389 p.Ala487Ser missense_variant 0.17
fbiC 1305392 p.Gly821Asp missense_variant 0.15
Rv1258c 1406377 p.Gly322Ser missense_variant 0.5
embR 1416225 p.Glu375* stop_gained 0.12
embR 1416315 c.1033C>A synonymous_variant 0.12
embR 1416737 p.Arg204Leu missense_variant 0.17
embR 1416909 p.Gly147Trp missense_variant 0.14
embR 1416916 c.430_431delGA frameshift_variant 0.18
embR 1416946 c.402C>G synonymous_variant 0.15
embR 1417160 p.Trp63Leu missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473413 n.-245G>T upstream_gene_variant 0.2
rrl 1475895 n.2238C>A non_coding_transcript_exon_variant 0.5
fabG1 1673397 c.-43T>C upstream_gene_variant 0.33
fabG1 1673485 p.Arg16Ser missense_variant 0.29
fabG1 1673707 p.Gly90Cys missense_variant 0.17
fabG1 1674134 p.Ile232Asn missense_variant 0.14
inhA 1674257 p.Ser19* stop_gained 0.22
inhA 1674340 p.Ile47Val missense_variant 0.4
rpsA 1833956 c.418_420delCTC conservative_inframe_deletion 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101879 c.1164C>T synonymous_variant 0.2
ndh 2102784 p.Gly87Cys missense_variant 0.5
ndh 2103000 c.42dupG frameshift_variant 0.4
katG 2154644 p.Gly490Cys missense_variant 0.25
katG 2155322 p.Ala264Ser missense_variant 0.67
katG 2156013 c.99C>T synonymous_variant 0.22
katG 2156371 c.-260C>A upstream_gene_variant 0.2
PPE35 2168930 c.1683G>A synonymous_variant 0.2
PPE35 2170205 c.408C>A synonymous_variant 0.2
Rv1979c 2222555 p.Pro204Ala missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518759 c.645C>A synonymous_variant 0.22
eis 2714248 p.Gly362Val missense_variant 0.33
folC 2746660 c.938delT frameshift_variant 0.25
folC 2746952 p.Lys216Arg missense_variant 0.29
folC 2747648 c.-50G>A upstream_gene_variant 0.22
folC 2747689 c.-91C>A upstream_gene_variant 0.25
folC 2747724 c.-126C>A upstream_gene_variant 0.17
pepQ 2859738 c.681C>A synonymous_variant 0.25
pepQ 2860484 c.-66G>T upstream_gene_variant 0.29
Rv2752c 3065615 p.Asp193Tyr missense_variant 0.22
Rv2752c 3065919 c.273G>A synonymous_variant 0.12
Rv2752c 3066238 c.-47C>A upstream_gene_variant 0.5
Rv2752c 3066300 c.-109G>T upstream_gene_variant 0.2
thyX 3067267 p.Phe227Leu missense_variant 0.18
thyX 3068008 c.-63G>T upstream_gene_variant 0.67
thyA 3073875 p.Phe199Leu missense_variant 0.29
ald 3086637 c.-183G>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087150 p.Gly111Cys missense_variant 0.67
Rv3083 3448999 p.Pro166Ala missense_variant 0.4
Rv3083 3449197 p.Arg232Ser missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474081 c.75C>T synonymous_variant 0.15
fprA 3474445 p.Gly147Cys missense_variant 0.14
fprA 3475332 c.1326C>A synonymous_variant 0.13
whiB7 3568605 c.75C>A synonymous_variant 0.18
whiB7 3568726 c.-47C>A upstream_gene_variant 0.13
whiB7 3568744 c.-65A>G upstream_gene_variant 0.15
Rv3236c 3612153 p.Gly322Trp missense_variant 0.33
Rv3236c 3612777 p.Asp114Tyr missense_variant 0.14
fbiA 3640895 p.Met118Thr missense_variant 0.13
fbiA 3641333 p.Gly264Val missense_variant 0.17
fbiB 3641789 c.255G>C synonymous_variant 0.15
fbiB 3641852 c.320dupG frameshift_variant 0.13
fbiB 3642189 p.Gly219Trp missense_variant 0.4
fbiB 3642263 c.729C>A synonymous_variant 0.29
fbiB 3642618 p.Asp362Tyr missense_variant 0.22
fbiB 3642672 p.Ala380Ser missense_variant 0.22
fbiB 3642835 p.Gly434Val missense_variant 0.29
alr 3840248 c.1173C>A synonymous_variant 0.2
alr 3840563 c.858G>T synonymous_variant 0.2
alr 3840629 c.792C>A synonymous_variant 0.18
alr 3840666 p.Arg252Leu missense_variant 0.14
rpoA 3877984 p.Thr175Asn missense_variant 0.29
rpoA 3878382 c.126G>T synonymous_variant 0.13
rpoA 3878423 p.Gly29* stop_gained 0.22
ddn 3986700 c.-144C>A upstream_gene_variant 0.13
ddn 3987164 c.321G>T synonymous_variant 0.29
clpC1 4038719 c.1986G>T synonymous_variant 0.5
clpC1 4039208 c.1497C>A synonymous_variant 0.12
clpC1 4040086 p.Arg207Cys missense_variant 0.17
clpC1 4040395 p.Gly104Trp missense_variant 0.17
clpC1 4040481 p.Ser75Phe missense_variant 0.2
panD 4044304 c.-23C>A upstream_gene_variant 0.22
embC 4242287 p.Leu809Ile missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243383 p.Ala51Ser missense_variant 0.22
embA 4244524 p.Pro431Gln missense_variant 0.15
embA 4245879 p.Asp883Tyr missense_variant 0.25
embA 4246200 c.2969_2970delAG frameshift_variant 0.18
embB 4246620 p.Ile36Thr missense_variant 0.25
embB 4247455 c.942C>A synonymous_variant 0.29
embB 4247461 c.949delT frameshift_variant 0.29
embB 4247464 c.951C>A synonymous_variant 0.29
embB 4249447 c.2934G>T synonymous_variant 0.22
aftB 4267131 p.Pro569His missense_variant 0.5
aftB 4268217 p.Trp207Leu missense_variant 0.18
aftB 4268685 c.151delC frameshift_variant 0.2
aftB 4269642 c.-806G>T upstream_gene_variant 0.17
ubiA 4269736 p.Leu33Pro missense_variant 0.29
ethR 4327138 c.-411C>A upstream_gene_variant 0.22
ethA 4327457 p.Asp6Gly missense_variant 0.4
ethR 4327612 p.Gly22Cys missense_variant 0.18
ethA 4327629 c.-156C>A upstream_gene_variant 0.18
ethR 4327670 p.Pro41Gln missense_variant 0.13
ethA 4328261 c.-788C>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407660 c.543G>T synonymous_variant 0.17
gid 4407999 c.203delT frameshift_variant 0.29
gid 4408220 c.-18G>T upstream_gene_variant 0.18