TB-Profiler result

Run: ERR4828450
Summary

Run ID: ERR4828450

Sample name:

Date: 01-04-2023 18:55:04

Number of reads: 4571021

Percentage reads mapped: 99.28

Strain: lineage1.1.1.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 1.0
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln 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 490972 p.Arg64Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 777581 p.Tyr300* stop_gained 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407148 p.Ala65Thr missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.18
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.18
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.21
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.15
rrl 1473764 n.107G>T non_coding_transcript_exon_variant 0.17
rrl 1474375 n.718G>A non_coding_transcript_exon_variant 0.2
rrl 1474418 n.761C>T non_coding_transcript_exon_variant 0.29
rrl 1474468 n.811G>A non_coding_transcript_exon_variant 0.2
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1474877 n.1220G>A non_coding_transcript_exon_variant 0.4
rrl 1475061 n.1404C>G non_coding_transcript_exon_variant 0.18
rrl 1475386 n.1729G>C non_coding_transcript_exon_variant 0.4
rrl 1475944 n.2287G>A non_coding_transcript_exon_variant 0.14
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.2
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.18
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.18
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.18
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476277 n.2620G>A non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476489 n.2832C>T non_coding_transcript_exon_variant 0.29
rpsA 1834319 p.Val260Ile missense_variant 1.0
rpsA 1834926 p.Gly462Ala missense_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918036 p.Arg33Cys missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156389 c.-278G>C upstream_gene_variant 1.0
katG 2156517 c.-406C>A upstream_gene_variant 0.8
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519074 c.960C>T synonymous_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859859 p.Ala187Glu missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_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
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
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 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 0.97
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246724 p.Leu71Met missense_variant 0.15
embB 4247028 p.Leu172Arg missense_variant 0.24
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
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408167 c.35_36insG frameshift_variant 0.89