TB-Profiler result

Run: SRR6045033
Summary

Run ID: SRR6045033

Sample name:

Date: 04-04-2023 11:51:41

Number of reads: 188606

Percentage reads mapped: 5.28

Strain:

Drug-resistance: HR-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
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620586 c.696C>T synonymous_variant 0.8
rpoB 760028 c.222C>A synonymous_variant 0.33
rpoB 760118 c.312T>C synonymous_variant 1.0
rpoB 761492 c.1686G>C synonymous_variant 0.29
rpoB 761510 c.1704T>C synonymous_variant 0.2
rpoB 761531 c.1725C>G synonymous_variant 0.22
rpoB 761537 c.1731C>G synonymous_variant 0.22
rpoB 761570 c.1764T>C synonymous_variant 0.29
rpoB 761573 c.1767C>G synonymous_variant 0.29
rpoB 761579 c.1773G>C synonymous_variant 0.29
rpoB 761606 c.1800C>G synonymous_variant 0.29
rpoB 762167 c.2361T>C synonymous_variant 0.33
rpoB 762176 c.2370T>C synonymous_variant 0.33
rpoB 762185 c.2379G>C synonymous_variant 0.33
rpoC 763169 c.-201A>G upstream_gene_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764650 c.1281G>T synonymous_variant 0.4
rpoC 764751 p.Val461Ala missense_variant 0.22
rpoC 764764 c.1395T>C synonymous_variant 0.43
rpoC 764815 c.1446A>G synonymous_variant 0.4
rpoC 764827 c.1458G>C synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777155 c.1326G>C synonymous_variant 1.0
mmpL5 778435 p.Asp16Tyr missense_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781682 c.123T>C synonymous_variant 0.33
rpsL 781715 c.156T>C synonymous_variant 0.29
rpsL 781763 c.204C>G synonymous_variant 0.25
rpsL 781766 c.207C>T synonymous_variant 0.25
rpsL 781772 c.213C>T synonymous_variant 0.25
rpsL 781808 c.249C>T synonymous_variant 0.3
rpsL 781811 c.252C>T synonymous_variant 0.3
rpsL 781814 c.255C>T synonymous_variant 0.27
rpsL 781817 c.258G>T synonymous_variant 0.27
rpsL 781827 c.268C>T synonymous_variant 0.2
rpsL 781832 c.273T>G synonymous_variant 0.22
rpsL 781859 c.300T>C synonymous_variant 0.25
rpsL 781868 c.309T>C synonymous_variant 0.29
rpsL 781871 c.312G>C synonymous_variant 0.29
rpsL 781892 c.333A>G synonymous_variant 0.29
rpsL 781916 c.357T>C synonymous_variant 0.29
rpsL 781929 p.Gly124Ser missense_variant 0.25
fbiC 1302948 c.18T>G synonymous_variant 1.0
Rv1258c 1407183 p.Leu53Pro missense_variant 0.33
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472194 n.349G>A non_coding_transcript_exon_variant 0.67
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrl 1473829 n.172G>C non_coding_transcript_exon_variant 1.0
rrl 1473831 n.174G>T non_coding_transcript_exon_variant 1.0
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 1.0
rrl 1473839 n.182G>A non_coding_transcript_exon_variant 1.0
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 1.0
rpsA 1833787 c.246C>G synonymous_variant 0.25
rpsA 1833790 c.249T>A synonymous_variant 0.25
rpsA 1833799 c.258C>G synonymous_variant 0.25
rpsA 1833811 c.270G>C synonymous_variant 0.25
rpsA 1833838 c.297G>C synonymous_variant 0.29
rpsA 1833841 c.300C>G synonymous_variant 0.29
rpsA 1833847 c.306C>G synonymous_variant 0.25
rpsA 1833856 c.315A>G synonymous_variant 0.29
rpsA 1833862 c.321G>T synonymous_variant 0.33
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 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170620 c.-8G>T upstream_gene_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.5
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726221 p.Phe10Cys missense_variant 0.4
folC 2746186 c.1413G>C synonymous_variant 0.25
folC 2746945 c.654C>A synonymous_variant 0.4
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3065829 p.Ile121Met missense_variant 1.0
Rv2752c 3066103 p.Asn30Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087534 p.Val239Phe missense_variant 0.4
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473903 c.-104A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640347 c.-196A>G upstream_gene_variant 0.15
fbiA 3640349 c.-194A>G upstream_gene_variant 0.15
fbiA 3640350 c.-193C>T upstream_gene_variant 0.15
fbiA 3640365 c.-178C>G upstream_gene_variant 0.17
fbiA 3640888 c.349delC frameshift_variant 0.29
alr 3840443 c.978G>A synonymous_variant 0.4
alr 3841546 c.-126C>A upstream_gene_variant 1.0
rpoA 3877587 c.921A>G synonymous_variant 0.25
rpoA 3877613 p.Ile299Val missense_variant 0.33
clpC1 4038767 c.1938G>C synonymous_variant 0.29
clpC1 4038770 c.1935C>T synonymous_variant 0.29
clpC1 4038773 c.1932T>C synonymous_variant 0.25
clpC1 4038782 c.1923G>T synonymous_variant 0.22
clpC1 4038790 c.1915C>T synonymous_variant 0.22
clpC1 4038809 p.Gln632His missense_variant 0.25
clpC1 4038812 c.1893T>C synonymous_variant 0.25
clpC1 4038815 c.1890G>T synonymous_variant 0.29
clpC1 4038878 c.1827A>G synonymous_variant 0.4
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245248 c.2016G>C synonymous_variant 0.33
embA 4245257 c.2025A>G synonymous_variant 0.67
embA 4245263 c.2031A>G synonymous_variant 0.5
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246101 p.Thr957Pro missense_variant 0.25
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269780 c.-944C>A upstream_gene_variant 0.67
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 0.8
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408114 c.19_88delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG frameshift_variant 1.0