TB-Profiler result

Run: ERR2229247
Summary

Run ID: ERR2229247

Sample name:

Date: 31-03-2023 16:52:26

Number of reads: 806149

Percentage reads mapped: 99.13

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrA 7129 c.-173T>C upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576463 c.1116G>A synonymous_variant 0.18
ccsA 619903 p.His5Tyr missense_variant 0.14
rpoC 766366 c.2997C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777884 c.597C>T synonymous_variant 0.15
mmpL5 777953 c.528T>G synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781605 p.Ile16Phe missense_variant 0.18
fbiC 1303615 p.Ala229Ser missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406238 p.Gly368Val missense_variant 0.12
Rv1258c 1406946 p.Ala132Gly missense_variant 0.11
Rv1258c 1407538 c.-198T>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.11
rrl 1476446 n.2789C>T non_coding_transcript_exon_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
rpsA 1833836 p.Arg99Trp missense_variant 0.15
rpsA 1833854 p.Lys105Glu missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153982 c.2130C>T synonymous_variant 0.22
PPE35 2167763 c.2850A>T synonymous_variant 0.14
PPE35 2167907 c.2706A>T synonymous_variant 0.2
PPE35 2168179 p.Pro812Ala missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169091 p.Val508Leu missense_variant 0.2
PPE35 2169101 c.1512G>C synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169457 p.His386Asp missense_variant 0.14
PPE35 2169902 p.Leu237Phe missense_variant 0.2
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.19
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2221723 p.Arg481Leu missense_variant 0.21
Rv1979c 2223186 c.-22C>G upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518340 p.Asp76Asn missense_variant 0.12
kasA 2519163 c.1050delC frameshift_variant 0.2
ribD 2987381 p.Gln181His missense_variant 0.12
fprA 3473890 c.-117C>G upstream_gene_variant 0.11
fprA 3474803 p.Arg266His missense_variant 0.22
whiB7 3568505 p.Arg59Trp missense_variant 0.18
fbiB 3640650 c.-885C>T upstream_gene_variant 0.2
alr 3840523 p.Ile300Val missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.24
rpoA 3878414 p.Tyr32His missense_variant 0.11
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039980 p.Leu242Pro missense_variant 0.11
panD 4044080 p.Val68Leu missense_variant 0.22
embC 4241618 p.Trp586Arg missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244615 c.1383G>A synonymous_variant 0.12
embB 4245677 c.-837G>T upstream_gene_variant 0.29
embB 4247028 p.Leu172Arg missense_variant 0.36
embB 4247379 p.Leu289Arg missense_variant 0.2
embB 4248041 p.Ala510Thr missense_variant 0.13
ubiA 4269624 p.Tyr70* stop_gained 0.13
ethA 4326468 p.Asp336Asn missense_variant 0.29
ethA 4327089 p.Leu129Ile missense_variant 0.2
ethA 4327518 c.-45G>A upstream_gene_variant 0.14
whiB6 4338261 c.261G>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407829 p.Gln125Pro missense_variant 0.11
gid 4408002 c.201T>C synonymous_variant 0.12
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0