TB-Profiler result

Run: ERR3468644
Summary

Run ID: ERR3468644

Sample name:

Date: 01-04-2023 02:20:05

Number of reads: 116785

Percentage reads mapped: 13.06

Strain: La1.8.1

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
La1.8 M.bovis None None 1.0
La1.8.1 M.bovis None 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
katG 2155693 p.Ser140Asn missense_variant 0.67 isoniazid
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 5752 c.513G>A synonymous_variant 1.0
gyrB 5929 c.690G>A synonymous_variant 0.25
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 762896 c.-474G>T upstream_gene_variant 0.4
rpoC 764479 c.1110G>A synonymous_variant 0.29
rpoC 764485 c.1116G>C synonymous_variant 0.29
rpoC 764498 p.Ser377Ala missense_variant 0.38
rpoC 764503 c.1134G>C synonymous_variant 0.38
rpoC 764527 c.1158C>T synonymous_variant 0.5
rpoC 764536 c.1167G>C synonymous_variant 0.5
rpoC 764537 p.Pro390Thr missense_variant 0.5
rpoC 764540 p.Val391Ile missense_variant 0.57
rpoC 764545 c.1176C>G synonymous_variant 0.57
rpoC 764548 c.1179G>C synonymous_variant 0.57
rpoC 764549 p.Pro394Ala missense_variant 0.57
rpoC 764552 p.Gly395Asn missense_variant 0.57
rpoC 764557 p.Asn396Lys missense_variant 0.57
rpoC 764575 c.1206T>G synonymous_variant 0.67
rpoC 764581 c.1212T>C synonymous_variant 0.67
rpoC 764582 p.Leu405Met missense_variant 0.67
rpoC 764587 c.1218C>G synonymous_variant 0.67
rpoC 764605 c.1236G>C synonymous_variant 0.8
rpoC 764611 c.1242G>T synonymous_variant 0.8
rpoC 764632 c.1263T>C synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
embR 1416795 p.Gly185Trp missense_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 1.0
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.6
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.6
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.8
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.6
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.75
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.6
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.5
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.33
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.5
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.5
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.5
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155590 c.522A>G synonymous_variant 0.67
katG 2155600 p.Cys171Val missense_variant 0.67
katG 2155608 p.Ala168Thr missense_variant 0.67
katG 2155613 p.Phe167Leu missense_variant 0.67
katG 2155614 p.Val166Ile missense_variant 0.67
katG 2155617 p.Ile165Met missense_variant 0.67
katG 2155626 c.486G>C synonymous_variant 0.67
katG 2155632 c.480A>G synonymous_variant 0.67
katG 2155637 p.Leu159Ile missense_variant 0.67
katG 2155655 p.Lys153Gln missense_variant 0.5
katG 2155661 p.Val151Ile missense_variant 0.5
katG 2155662 c.450G>C synonymous_variant 0.5
katG 2155670 c.442C>T synonymous_variant 0.5
katG 2155674 c.438G>C synonymous_variant 0.5
katG 2155680 c.432G>C synonymous_variant 0.5
katG 2155691 c.421T>C synonymous_variant 0.5
katG 2155696 p.Ala139Gly missense_variant 0.67
katG 2155716 c.396T>G synonymous_variant 0.67
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242680 p.Ala940Ser missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0