TB-Profiler result

Run: ERR2653059
Summary

Run ID: ERR2653059

Sample name:

Date: 31-03-2023 22:28:28

Number of reads: 637033

Percentage reads mapped: 99.16

Strain: lineage4.3.2

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 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 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
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 5321 p.Lys28Glu missense_variant 0.12
gyrA 7303 c.2T>C start_lost 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7748 c.447A>G synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575225 c.-123T>A upstream_gene_variant 0.14
mshA 575384 p.Ile13Val missense_variant 0.2
ccsA 620100 c.210G>C synonymous_variant 0.22
ccsA 620152 p.Ile88Phe missense_variant 0.2
rpoB 760233 p.Ser143Arg missense_variant 0.33
rpoB 760366 p.Lys187Arg missense_variant 0.14
rpoC 763512 p.Cys48Phe missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765022 c.1653G>A synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.12
rpoC 765360 p.Ala664Val missense_variant 1.0
rpoC 765789 p.Ala807Asp missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775882 c.2598delC frameshift_variant 0.15
mmpL5 775906 p.Lys859Glu missense_variant 0.13
mmpL5 776282 c.2199G>A synonymous_variant 0.12
mmpL5 777479 c.1002C>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801457 p.Lys217* stop_gained 0.12
fbiC 1303760 p.Ile277Asn missense_variant 0.4
fbiC 1303766 p.Lys279Met missense_variant 0.4
embR 1416276 p.Arg358Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472430 n.585C>G non_coding_transcript_exon_variant 0.11
rrl 1473736 n.83delG non_coding_transcript_exon_variant 0.11
rrl 1476555 n.2898A>T non_coding_transcript_exon_variant 0.2
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14
rpsA 1834390 c.849G>A synonymous_variant 0.11
rpsA 1834937 p.Ser466Gly missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101891 c.1152C>T synonymous_variant 0.12
katG 2153996 p.Ala706Thr missense_variant 0.12
katG 2155806 c.306T>C synonymous_variant 0.25
Rv1979c 2221771 p.Leu465Pro missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289874 c.-633C>A upstream_gene_variant 0.11
eis 2714186 p.Leu383Ile missense_variant 0.13
eis 2714233 p.Ser367Leu missense_variant 0.11
eis 2715024 c.309A>G synonymous_variant 1.0
folC 2747026 c.573C>G synonymous_variant 0.11
pepQ 2860174 p.Tyr82Phe missense_variant 0.12
ribD 2987000 c.162C>T synonymous_variant 0.18
ribD 2987423 c.585G>T synonymous_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339428 p.Ala104Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474410 p.His135Arg missense_variant 0.11
Rv3236c 3612746 p.Val124Ala missense_variant 0.14
fbiA 3640486 c.-57G>A upstream_gene_variant 0.15
fbiB 3640806 c.-729C>A upstream_gene_variant 0.25
fbiB 3641643 p.Ala37Ser missense_variant 0.17
alr 3841568 c.-148G>A upstream_gene_variant 1.0
alr 3841570 c.-151delA upstream_gene_variant 1.0
alr 3841574 c.-154T>G upstream_gene_variant 1.0
alr 3841578 c.-158G>T upstream_gene_variant 1.0
alr 3841582 c.-162A>G upstream_gene_variant 1.0
alr 3841584 c.-164C>A upstream_gene_variant 1.0
alr 3841589 c.-170delG upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
rpoA 3877492 p.Gln339Leu missense_variant 0.18
rpoA 3878000 p.Pro170Thr missense_variant 0.11
rpoA 3878630 c.-123G>C upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044210 c.72C>A synonymous_variant 0.22
panD 4044274 p.Arg3Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244476 p.Ala415Glu missense_variant 0.13
embB 4246196 c.-318C>A upstream_gene_variant 0.14
embB 4246739 p.Pro76Thr missense_variant 0.12
embB 4248205 c.1692C>A synonymous_variant 0.12
embB 4249434 p.Leu974Pro missense_variant 0.14
aftB 4266995 c.1842G>T synonymous_variant 0.22
aftB 4267428 p.Ser470Trp missense_variant 0.11
aftB 4268579 c.258G>A synonymous_variant 0.18
aftB 4268791 c.46C>T synonymous_variant 0.91
ethA 4327241 p.Gly78Asp missense_variant 0.17
ethR 4327567 p.Ser7Cys missense_variant 0.15
whiB6 4338512 p.Ala4Ser missense_variant 1.0
whiB6 4338513 p.Tyr3* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407555 c.648A>G synonymous_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0