TB-Profiler result

Run: ERR4815515
Summary

Run ID: ERR4815515

Sample name:

Date: 01-04-2023 13:54:29

Number of reads: 2002534

Percentage reads mapped: 84.18

Strain: lineage4.1.3;lineage1.1.2

Drug-resistance: Sensitive

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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 0.71
lineage1 Indo-Oceanic EAI RD239 0.23
lineage4.1 Euro-American T;X;H None 0.72
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.21
lineage4.1.3 Euro-American T;X;H None 0.65
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.2
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
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 6112 p.Met291Ile missense_variant 0.17
gyrB 6124 c.885C>T synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.98
gyrA 8435 c.1134C>G synonymous_variant 0.25
gyrA 8452 p.Ala384Val missense_variant 0.24
gyrA 8636 c.1335A>C synonymous_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 0.22
mshA 575376 p.Ser10Leu missense_variant 0.26
rpoB 760223 c.417T>C synonymous_variant 0.13
rpoB 760235 c.429T>C synonymous_variant 0.16
rpoB 760283 c.477G>C synonymous_variant 0.14
rpoB 760406 c.600G>C synonymous_variant 0.16
rpoB 760424 c.618C>G synonymous_variant 0.14
rpoB 760430 c.624T>C synonymous_variant 0.18
rpoB 760646 c.840C>G synonymous_variant 0.13
rpoB 760928 c.1122G>C synonymous_variant 0.15
rpoB 760946 c.1140A>G synonymous_variant 0.16
rpoB 761102 c.1296A>G synonymous_variant 0.15
rpoB 761354 c.1548C>T synonymous_variant 0.15
rpoB 762014 c.2208C>T synonymous_variant 0.13
rpoB 762293 c.2487T>C synonymous_variant 0.13
rpoC 762929 c.-441G>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 0.16
rpoC 763546 c.177A>G synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.15
rpoC 763675 c.306C>G synonymous_variant 0.16
rpoC 763702 c.333C>G synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.13
rpoC 763872 p.Gly168Ala missense_variant 0.15
rpoC 763876 p.Glu169Asp missense_variant 0.16
rpoC 763879 c.510A>G synonymous_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 0.16
rpoC 763886 c.517C>A synonymous_variant 0.16
rpoC 764752 c.1383G>C synonymous_variant 0.15
rpoC 764764 c.1395T>C synonymous_variant 0.18
rpoC 764815 c.1446A>G synonymous_variant 0.16
rpoC 764827 c.1458G>C synonymous_variant 0.15
rpoC 764888 c.1519T>C synonymous_variant 0.14
rpoC 765019 c.1650A>G synonymous_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 0.74
rpoC 765171 p.Pro601Leu missense_variant 0.28
rpoC 765421 c.2052C>G synonymous_variant 0.13
rpoC 767098 c.3729T>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.79
fbiC 1304610 c.1680C>T synonymous_variant 0.72
fbiC 1304817 c.1887T>C synonymous_variant 0.16
fbiC 1304829 c.1899T>C synonymous_variant 0.2
fbiC 1304832 c.1902C>T synonymous_variant 0.15
fbiC 1304856 c.1926C>G synonymous_variant 0.44
fbiC 1304862 c.1932G>A synonymous_variant 0.16
fbiC 1304869 c.1939C>T synonymous_variant 0.18
fbiC 1304875 p.Ile649Val missense_variant 0.17
fbiC 1304891 p.Ile654Thr missense_variant 0.13
fbiC 1304893 p.Gly655Ser missense_variant 0.13
fbiC 1304907 c.1977C>G synonymous_variant 0.13
fbiC 1304910 c.1980G>C synonymous_variant 0.15
fbiC 1304916 c.1986T>C synonymous_variant 0.16
fbiC 1304928 c.1998T>C synonymous_variant 0.18
fbiC 1304937 c.2007G>C synonymous_variant 0.17
fbiC 1304958 c.2028T>G synonymous_variant 0.21
fbiC 1304983 c.2053C>T synonymous_variant 0.15
fbiC 1304994 c.2064A>G synonymous_variant 0.16
fbiC 1304995 p.Leu689Met missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.13
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.18
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.21
rrl 1474291 n.635_649delTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.25
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.21
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.31
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.17
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.14
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.19
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.18
rrl 1474743 n.1086T>G non_coding_transcript_exon_variant 0.17
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.21
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.18
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.22
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 0.14
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.13
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.14
rpsA 1833661 c.120A>G synonymous_variant 0.17
rpsA 1833667 c.126C>G synonymous_variant 0.17
rpsA 1833727 c.186G>C synonymous_variant 0.12
rpsA 1833742 c.201A>G synonymous_variant 0.19
rpsA 1833745 c.204G>C synonymous_variant 0.18
rpsA 1833748 c.207C>G synonymous_variant 0.21
rpsA 1833787 c.246C>G synonymous_variant 0.18
rpsA 1833790 c.249T>C synonymous_variant 0.18
rpsA 1833802 c.261A>G synonymous_variant 0.2
rpsA 1833928 c.387G>C synonymous_variant 0.15
rpsA 1834366 c.825A>G synonymous_variant 0.12
rpsA 1834528 c.987T>C synonymous_variant 0.13
rpsA 1834690 c.1149T>C synonymous_variant 0.14
rpsA 1834765 p.Glu408Asp missense_variant 0.13
rpsA 1834775 p.Ala412Thr missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 0.23
PPE35 2167983 p.Gly877Asp missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.2
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18
ahpC 2726638 p.Ala149Val missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 0.23
Rv2752c 3066376 c.-185C>T upstream_gene_variant 0.21
thyX 3067316 c.630A>G synonymous_variant 0.14
thyX 3067349 c.597G>C synonymous_variant 0.14
thyX 3067355 c.591A>C synonymous_variant 0.14
thyA 3074205 p.Glu89Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.95
fprA 3474597 c.591C>A synonymous_variant 0.35
fprA 3475159 p.Asn385Asp missense_variant 0.27
rpoA 3878490 c.18C>A synonymous_variant 0.14
clpC1 4038596 c.2109A>G synonymous_variant 0.15
clpC1 4038623 c.2082A>G synonymous_variant 0.13
clpC1 4039694 c.1011G>C synonymous_variant 0.18
clpC1 4039724 c.981A>G synonymous_variant 0.16
clpC1 4039865 c.840T>C synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 0.23
embC 4241042 p.Asn394Asp missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.64
embA 4243848 p.Val206Met missense_variant 0.29
embA 4245146 c.1914G>A synonymous_variant 0.14
embA 4245149 c.1917C>G synonymous_variant 0.14
embA 4245153 p.Ile641Val missense_variant 0.14
embA 4245182 c.1950T>C synonymous_variant 0.14
embA 4245189 c.1957C>T synonymous_variant 0.15
embA 4245198 p.Leu656Ile missense_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 0.18
embB 4247356 c.843C>T synonymous_variant 0.26
embB 4247646 p.Glu378Ala missense_variant 0.18
aftB 4268683 p.Gly52Ser missense_variant 0.62
ubiA 4269387 p.Glu149Asp missense_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 0.16
whiB6 4338441 p.Tyr27* stop_gained 0.3
whiB6 4338449 p.Ala25Pro missense_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.19
gid 4407588 c.615A>G synonymous_variant 0.15
gid 4407873 c.330G>T synonymous_variant 0.18