TB-Profiler result

Run: ERR2245296
Summary

Run ID: ERR2245296

Sample name:

Date: 31-03-2023 17:37:55

Number of reads: 2637791

Percentage reads mapped: 96.66

Strain: lineage3.1.1

Drug-resistance: RR-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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
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
gyrB 5994 p.His252Arg missense_variant 0.15
gyrB 7074 p.Gly612Val missense_variant 0.13
gyrA 7286 c.-16T>C upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8288 c.987T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491603 p.Ala274Val missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575186 c.-162C>A upstream_gene_variant 0.18
mshA 575487 p.Val47Gly missense_variant 0.2
mshA 576034 c.687T>C synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.37
mshA 576111 p.Ala255Gly missense_variant 0.26
mshA 576589 c.1242A>T synonymous_variant 0.18
mshA 576724 c.1378dupA frameshift_variant 0.17
ccsA 620520 c.630C>T synonymous_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760405 p.Pro200Gln missense_variant 0.14
rpoB 761292 p.Val496Met missense_variant 1.0
rpoB 761849 p.Cys681* stop_gained 0.18
rpoB 762346 p.Phe847Tyr missense_variant 0.12
rpoB 762433 p.Gly876Val missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767260 p.Phe1297Leu missense_variant 0.2
mmpL5 775587 c.2894G>T stop_lost&splice_region_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776219 c.2262C>A synonymous_variant 0.13
mmpL5 777041 p.Arg480Leu missense_variant 0.13
mmpL5 777061 p.Ala474Pro missense_variant 0.12
mmpL5 778926 c.-446A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303131 p.Asp67Glu missense_variant 0.14
fbiC 1304016 c.1086C>A synonymous_variant 0.15
fbiC 1304379 c.1449G>T synonymous_variant 0.15
fbiC 1305029 p.Val700Ala missense_variant 0.13
Rv1258c 1407039 p.Val101Gly missense_variant 0.27
Rv1258c 1407144 p.Val66Gly missense_variant 0.33
embR 1416622 p.Asp242Glu missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473310 n.1465T>G non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.67
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.67
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.5
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
fabG1 1673243 c.-197G>C upstream_gene_variant 0.11
rpsA 1833792 p.Asp84Gly missense_variant 0.15
rpsA 1833884 p.Thr115Ala missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101866 p.Trp393Arg missense_variant 0.15
ndh 2101889 p.Val385Gly missense_variant 0.15
ndh 2102137 c.906G>T synonymous_variant 0.16
ndh 2102773 c.270C>A synonymous_variant 0.18
ndh 2102952 p.Lys31Glu missense_variant 0.18
katG 2154043 p.Thr690Asn missense_variant 0.22
katG 2154078 c.2034C>T synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156265 c.-154G>T upstream_gene_variant 0.2
katG 2156372 c.-261C>A upstream_gene_variant 0.15
PPE35 2167752 p.Ala954Asp missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168110 p.Thr835Ala missense_variant 0.14
PPE35 2168119 c.2493delT frameshift_variant 0.18
PPE35 2170461 p.Gly51Glu missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>G upstream_gene_variant 0.2
pncA 2288734 p.Ala170Thr missense_variant 0.18
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519128 c.1014G>T synonymous_variant 0.18
eis 2714296 p.Ala346Val missense_variant 0.29
eis 2714762 p.Leu191Ile missense_variant 0.14
eis 2715558 c.-226A>C upstream_gene_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
folC 2746396 c.1203C>A synonymous_variant 0.17
folC 2746779 p.Gly274Cys missense_variant 0.29
pepQ 2859910 p.Arg170Leu missense_variant 0.13
pepQ 2860261 p.Val53Gly missense_variant 0.13
pepQ 2860270 p.Arg50Leu missense_variant 0.13
ribD 2987540 c.702G>T synonymous_variant 0.14
Rv2752c 3065162 p.Asn344Asp missense_variant 0.12
Rv2752c 3065632 p.Gly187Asp missense_variant 0.18
Rv2752c 3065918 p.Phe92Ile missense_variant 0.25
thyX 3067470 p.Asn159Thr missense_variant 0.2
thyX 3067535 p.Asp137Glu missense_variant 0.22
thyX 3067670 p.Glu92Asp missense_variant 0.14
thyA 3074395 p.Thr26Ile missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086992 p.Val58Ala missense_variant 0.29
fbiD 3339450 c.333T>C synonymous_variant 0.12
fbiD 3339598 p.Arg161Trp missense_variant 0.22
Rv3083 3449288 p.Pro262His missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474627 p.Phe207Leu missense_variant 0.23
Rv3236c 3612012 p.Leu369Met missense_variant 0.2
fbiA 3640691 p.Asp50Ala missense_variant 0.5
fbiB 3641904 p.Asp124Tyr missense_variant 0.25
alr 3841027 p.Val132Leu missense_variant 0.18
rpoA 3877882 p.Ala209Glu missense_variant 0.13
rpoA 3878470 p.Val13Asp missense_variant 0.29
ddn 3986821 c.-23C>T upstream_gene_variant 0.2
ddn 3986912 c.69G>T synonymous_variant 0.12
ddn 3986935 p.Arg31His missense_variant 0.14
clpC1 4038166 p.Ala847Thr missense_variant 0.12
clpC1 4039162 p.His515Asp missense_variant 0.1
clpC1 4039602 p.Ala368Glu missense_variant 0.2
clpC1 4040034 p.Ala224Gly missense_variant 0.15
embC 4240044 p.Trp61* stop_gained 0.17
embC 4240136 p.Ala92Ser missense_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240495 c.633T>G synonymous_variant 0.25
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243840 p.Lys203Met missense_variant 0.12
embA 4243863 p.Val211Leu missense_variant 0.12
embA 4245561 p.Val777Leu missense_variant 0.22
embA 4245681 p.Gly817Cys missense_variant 0.5
embA 4245930 p.Gly900Cys missense_variant 0.13
embB 4245986 c.-528G>T upstream_gene_variant 0.13
embB 4246058 c.-456C>T upstream_gene_variant 0.13
embA 4246170 p.Asp980Tyr missense_variant 0.22
embB 4246530 p.Ser6Ile missense_variant 0.25
embB 4247028 p.Leu172Gln missense_variant 0.29
embB 4248343 c.1830G>A synonymous_variant 0.12
embB 4248656 p.Ala715Ser missense_variant 0.13
embB 4249212 p.Leu900Pro missense_variant 0.12
aftB 4267900 p.Ala313Ser missense_variant 0.38
aftB 4267975 p.Ser288Ala missense_variant 0.18
aftB 4268623 p.Trp72Gly missense_variant 0.25
aftB 4268675 c.162A>T synonymous_variant 0.22
ethA 4327470 p.Thr2Ala missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0