TB-Profiler result

Run: SRR6257069
Summary

Run ID: SRR6257069

Sample name:

Date: 04-04-2023 13:25:14

Number of reads: 602934

Percentage reads mapped: 93.6

Strain: lineage2.2

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288688 p.Ser185Thr missense_variant 0.17 pyrazinamide
folC 2747480 p.Glu40Gly missense_variant 1.0 para-aminosalicylic_acid
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 6043 p.Lys268Asn missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8055 c.754C>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9668 c.2367C>T synonymous_variant 0.17
fgd1 490716 c.-67G>T upstream_gene_variant 0.15
fgd1 490742 c.-41C>T upstream_gene_variant 0.13
fgd1 490744 c.-39T>C upstream_gene_variant 0.13
fgd1 490748 c.-35G>T upstream_gene_variant 0.13
fgd1 490994 p.Gly71Asp missense_variant 0.22
fgd1 491569 p.Asp263Asn missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.75
mshA 575204 c.-144C>A upstream_gene_variant 0.22
mshA 575216 c.-132C>A upstream_gene_variant 0.22
mshA 575363 p.His6Asp missense_variant 0.5
mshA 575419 c.72C>A synonymous_variant 0.5
mshA 575423 p.Arg26Ser missense_variant 0.5
mshA 575805 p.Ser153Leu missense_variant 0.67
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.88
rpoB 759836 c.30C>A synonymous_variant 0.14
rpoB 761242 p.Pro479Leu missense_variant 0.29
rpoB 761292 p.Val496Met missense_variant 0.29
rpoB 761405 p.His533Gln missense_variant 0.4
rpoB 762010 p.Leu735Gln missense_variant 0.15
rpoB 762048 p.Glu748* stop_gained 0.2
rpoB 762117 p.Ser771Pro missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.82
rpoC 764918 p.Val517Leu missense_variant 1.0
rpoC 765739 c.2370G>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776698 p.Pro595Thr missense_variant 0.18
mmpL5 777164 c.1317C>T synonymous_variant 0.33
mmpL5 777322 p.Val387Ile missense_variant 0.22
mmpL5 778090 p.Gly131Trp missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801410 p.Arg201His missense_variant 0.13
fbiC 1302889 c.-42G>T upstream_gene_variant 0.15
fbiC 1303672 p.Ala248Ser missense_variant 0.17
fbiC 1305069 c.2139G>T synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416232 p.Cys372Gly missense_variant 0.18
embR 1416989 c.358delA frameshift_variant 0.22
embR 1417033 c.315C>T synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.47
rpsA 1833683 p.Arg48Trp missense_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918320 c.381G>T synonymous_variant 0.18
ndh 2102355 p.Gln230Lys missense_variant 0.18
ndh 2102690 p.Ala118Asp missense_variant 0.12
ndh 2103077 c.-35G>T upstream_gene_variant 0.33
ndh 2103149 c.-107G>T upstream_gene_variant 0.22
ndh 2103152 c.-110G>T upstream_gene_variant 0.22
ndh 2103174 c.-133delG upstream_gene_variant 0.29
katG 2154405 c.1707G>T synonymous_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156343 c.-232A>G upstream_gene_variant 0.14
PPE35 2167814 c.2799C>T synonymous_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.24
PPE35 2167868 c.2745A>C synonymous_variant 0.24
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2168437 p.Leu726Ile missense_variant 0.13
PPE35 2169457 p.His386Asp missense_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.31
PPE35 2170053 p.Thr187Ser missense_variant 0.36
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170220 c.393C>G synonymous_variant 0.13
PPE35 2170223 c.390T>C synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289635 c.-394G>T upstream_gene_variant 0.22
kasA 2518675 p.Met187Ile missense_variant 0.22
kasA 2518809 p.Lys232Arg missense_variant 0.4
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.17
eis 2714787 p.Trp182Cys missense_variant 0.22
ahpC 2726350 p.Trp53Leu missense_variant 0.43
pepQ 2860186 p.Ala78Val missense_variant 0.18
ribD 2987026 p.Ala63Gly missense_variant 0.22
Rv2752c 3064519 p.Val558Gly missense_variant 0.29
Rv2752c 3066026 p.Gly56Ser missense_variant 0.22
Rv2752c 3066304 c.-113C>A upstream_gene_variant 0.17
Rv2752c 3066336 c.-145C>A upstream_gene_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087310 p.Pro164His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568582 p.Pro33Gln missense_variant 0.12
whiB7 3568753 c.-74G>A upstream_gene_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641490 c.-45G>T upstream_gene_variant 0.67
fbiB 3641874 p.Gly114Cys missense_variant 0.25
fbiB 3641900 c.366G>T synonymous_variant 0.25
fbiB 3642513 p.Pro327Ser missense_variant 0.17
fbiB 3642616 p.Pro361His missense_variant 0.3
alr 3840603 p.Pro273Leu missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 0.16
rpoA 3877558 p.Pro317His missense_variant 0.13
ddn 3986822 c.-22C>A upstream_gene_variant 0.18
ddn 3986848 p.Pro2Gln missense_variant 0.22
embC 4239966 p.Val35Glu missense_variant 0.15
embC 4240300 p.Gln146His missense_variant 0.25
embC 4241459 p.Arg533Cys missense_variant 1.0
embC 4242156 p.Met765Lys missense_variant 0.5
embA 4242301 c.-932G>T upstream_gene_variant 0.4
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245187 p.Thr652Lys missense_variant 0.2
embA 4245215 c.1983A>T synonymous_variant 0.17
embA 4245395 c.2163C>A synonymous_variant 0.22
embA 4245498 p.Gln756* stop_gained 0.33
embB 4246960 c.447G>A synonymous_variant 0.17
embB 4247031 p.Arg173His missense_variant 0.25
embB 4247470 c.957T>C synonymous_variant 0.18
embB 4247472 p.Phe320Tyr missense_variant 0.18
embB 4249669 c.3156C>T synonymous_variant 0.22
embB 4249778 p.Trp1089Arg missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267903 p.Val312Leu missense_variant 0.4
aftB 4268278 p.Pro187Thr missense_variant 0.22
ubiA 4269999 c.-166G>T upstream_gene_variant 0.25
ethA 4326869 p.Val202Gly missense_variant 1.0
ethA 4327093 p.Ser127Arg missense_variant 0.22
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.82
gid 4407927 p.Glu92Asp missense_variant 1.0