TB-Profiler result

Run: ERR4798898
Summary

Run ID: ERR4798898

Sample name:

Date: 01-04-2023 08:43:09

Number of reads: 2180610

Percentage reads mapped: 88.83

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.98
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.98
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.98
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 761139 p.His445Asp missense_variant 0.9 rifampicin
katG 2155168 p.Ser315Asn missense_variant 0.98 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.97
rpoB 760139 c.333A>G synonymous_variant 0.12
rpoB 760571 c.765G>C synonymous_variant 0.12
rpoB 761027 c.1221A>C synonymous_variant 0.11
rpoB 761036 c.1230G>C synonymous_variant 0.11
rpoB 761037 c.1231T>C synonymous_variant 0.11
rpoB 761051 c.1245G>T synonymous_variant 0.12
rpoB 761054 c.1248G>C synonymous_variant 0.12
rpoB 761057 c.1251G>C synonymous_variant 0.12
rpoB 761060 c.1254C>G synonymous_variant 0.12
rpoB 761063 c.1257C>G synonymous_variant 0.12
rpoB 761084 c.1278C>A synonymous_variant 0.14
rpoB 762101 c.2295C>G synonymous_variant 0.11
rpoB 762158 c.2352G>C synonymous_variant 0.11
rpoB 762167 c.2361T>C synonymous_variant 0.12
rpoB 762185 c.2379G>C synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763492 c.123G>C synonymous_variant 0.11
rpoC 763528 c.159G>A synonymous_variant 0.14
rpoC 763546 c.177A>G synonymous_variant 0.12
rpoC 763570 c.201G>C synonymous_variant 0.12
rpoC 764452 c.1083T>C synonymous_variant 0.12
rpoC 764458 c.1089G>C synonymous_variant 0.12
rpoC 764461 c.1092A>G synonymous_variant 0.12
rpoC 764497 c.1128A>G synonymous_variant 0.13
rpoC 764521 c.1152T>C synonymous_variant 0.14
rpoC 764527 c.1158C>T synonymous_variant 0.13
rpoC 764530 c.1161C>T synonymous_variant 0.14
rpoC 764533 c.1164C>A synonymous_variant 0.13
rpoC 764536 c.1167G>T synonymous_variant 0.13
rpoC 764539 c.1170C>G synonymous_variant 0.13
rpoC 764548 c.1179G>A synonymous_variant 0.15
rpoC 764554 c.1185C>T synonymous_variant 0.18
rpoC 764566 c.1197C>G synonymous_variant 0.2
rpoC 764575 c.1206T>G synonymous_variant 0.19
rpoC 764605 c.1236G>C synonymous_variant 0.16
rpoC 764611 c.1242G>T synonymous_variant 0.18
rpoC 764623 c.1254C>T synonymous_variant 0.17
rpoC 764626 c.1257C>T synonymous_variant 0.17
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.13
rpoC 764716 c.1347G>C synonymous_variant 0.11
rpoC 764746 c.1377G>T synonymous_variant 0.11
rpoC 764752 c.1383G>C synonymous_variant 0.13
rpoC 764758 c.1389C>G synonymous_variant 0.12
rpoC 764764 c.1395T>C synonymous_variant 0.14
rpoC 764803 c.1434C>T synonymous_variant 0.12
rpoC 764810 p.Pro481Ala missense_variant 0.12
rpoC 764815 c.1446A>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.17
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.27
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.27
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.27
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.25
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.45
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.45
rrs 1472846 n.1001C>T non_coding_transcript_exon_variant 0.18
rrs 1472847 n.1002G>A non_coding_transcript_exon_variant 0.18
rrs 1472860 n.1015C>T non_coding_transcript_exon_variant 0.23
rrs 1472861 n.1016G>A non_coding_transcript_exon_variant 0.23
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.36
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.44
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.44
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.44
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.44
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.44
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.43
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.43
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.2
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.11
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.17
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.17
rrl 1473414 n.-244G>C upstream_gene_variant 1.0
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.17
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.18
rrl 1474181 n.524_525insT non_coding_transcript_exon_variant 0.2
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 0.2
rrl 1474185 n.529delA non_coding_transcript_exon_variant 0.2
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.2
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.2
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.22
rrl 1474413 n.756A>C non_coding_transcript_exon_variant 0.25
rrl 1475426 n.1769C>A non_coding_transcript_exon_variant 0.29
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.29
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.14
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.13
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
pncA 2289365 c.-125delC upstream_gene_variant 0.95
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
rpoA 3878184 c.324C>T synonymous_variant 0.12
rpoA 3878193 c.315T>C synonymous_variant 0.12
rpoA 3878197 p.Glu104Ala missense_variant 0.1
rpoA 3878217 c.291A>G synonymous_variant 0.11
rpoA 3878244 c.264G>A synonymous_variant 0.12
rpoA 3878259 c.249G>C synonymous_variant 0.12
rpoA 3878271 c.237T>C synonymous_variant 0.1
clpC1 4039106 c.1599G>C synonymous_variant 0.1
clpC1 4039136 c.1569C>T synonymous_variant 0.11
clpC1 4039145 c.1560G>C synonymous_variant 0.11
clpC1 4039925 c.780C>G synonymous_variant 0.13
clpC1 4039931 c.774T>C synonymous_variant 0.12
clpC1 4040048 c.657C>T synonymous_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040090 p.Ser205Cys missense_variant 0.11
clpC1 4040202 p.Ser168Phe missense_variant 0.94
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0