TB-Profiler result

Run: ERR2229477
Summary

Run ID: ERR2229477

Sample name:

Date: 31-03-2023 17:14:40

Number of reads: 728017

Percentage reads mapped: 99.07

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 0.99
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 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.14
gyrA 7271 c.-31A>G upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8777 p.Asp492Glu missense_variant 0.12
fgd1 491330 p.Lys183Met missense_variant 0.14
fgd1 491353 p.Gly191Ser missense_variant 0.18
ccsA 619916 c.28delC frameshift_variant 0.33
ccsA 620185 p.Gly99Ser missense_variant 0.15
rpoB 759814 c.10dupT frameshift_variant 0.15
rpoB 761164 p.Gly453Val missense_variant 0.12
rpoC 763369 c.-1C>T upstream_gene_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.15
mmpL5 775727 c.2754C>G synonymous_variant 0.15
mmpL5 775736 c.2745C>G synonymous_variant 0.15
mmpL5 775741 c.2740C>T synonymous_variant 0.17
mmpL5 775742 c.2739C>T synonymous_variant 0.17
mmpL5 775747 p.Met912Leu missense_variant 0.17
mmpL5 775748 c.2733T>C synonymous_variant 0.17
mmpL5 775851 p.Ser877Thr missense_variant 0.17
mmpL5 775853 c.2628C>T synonymous_variant 0.17
mmpL5 775857 p.Gly875Ala missense_variant 0.17
mmpL5 775862 c.2619G>C synonymous_variant 0.17
mmpL5 776417 c.2064G>C synonymous_variant 0.18
mmpL5 776433 p.Ser683Leu missense_variant 0.22
mmpL5 777566 c.915C>G synonymous_variant 0.25
mmpL5 777571 p.Gly304Arg missense_variant 0.29
mmpL5 777573 p.Phe303Tyr missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407233 c.108G>A synonymous_variant 0.12
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.12
Rv1258c 1407243 p.Leu33Gln missense_variant 0.12
atpE 1461041 c.-4G>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474719 n.1062G>T non_coding_transcript_exon_variant 0.13
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.13
rrl 1476172 n.2515G>C non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.22
fabG1 1673349 c.-91G>C upstream_gene_variant 0.27
fabG1 1673357 c.-83G>A upstream_gene_variant 0.27
fabG1 1673359 c.-81T>C upstream_gene_variant 0.27
fabG1 1673361 c.-79C>G upstream_gene_variant 0.27
fabG1 1673380 c.-60C>G upstream_gene_variant 0.47
inhA 1674816 c.618_619dupGC frameshift_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918194 c.255C>A synonymous_variant 0.25
katG 2156442 c.-331G>T upstream_gene_variant 0.2
katG 2156466 c.-355G>T upstream_gene_variant 0.13
PPE35 2167955 c.2658A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168281 p.Pro778Ser missense_variant 0.13
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.19
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.48
PPE35 2170371 p.Thr81Val missense_variant 0.12
PPE35 2170385 c.228G>T synonymous_variant 0.12
PPE35 2170392 p.Gly74Ala missense_variant 0.11
PPE35 2170400 c.213G>C synonymous_variant 0.22
PPE35 2170412 c.201G>A synonymous_variant 0.18
PPE35 2170415 c.198A>G synonymous_variant 0.18
Rv1979c 2221963 p.Ala401Glu missense_variant 0.12
Rv1979c 2221987 p.Leu393Pro missense_variant 0.12
Rv1979c 2223136 p.Ala10Gly missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518240 c.126C>T synonymous_variant 0.14
kasA 2518839 p.Ala242Gly missense_variant 0.12
kasA 2518843 c.729T>C synonymous_variant 0.12
kasA 2519363 c.1249T>C stop_lost&splice_region_variant 0.15
folC 2747575 c.24G>A synonymous_variant 0.29
Rv2752c 3065623 p.Arg190Gln missense_variant 0.12
Rv2752c 3065925 c.267G>A synonymous_variant 0.13
thyX 3067362 p.Phe195Ser missense_variant 0.13
whiB7 3568469 p.Phe71Ile missense_variant 0.2
Rv3236c 3611962 p.Asn385Lys missense_variant 0.12
fbiB 3640749 c.-786G>C upstream_gene_variant 0.11
fbiA 3640880 p.Leu113Arg missense_variant 0.3
fbiA 3640888 c.349delC frameshift_variant 0.25
fbiB 3641223 c.-312C>T upstream_gene_variant 0.14
fbiB 3642143 c.611delT frameshift_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4038239 c.2466T>C synonymous_variant 0.11
clpC1 4039354 p.Arg451Cys missense_variant 0.14
clpC1 4039691 c.1014G>C synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242655 c.-578A>G upstream_gene_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.56
embB 4246548 p.Pro12Gln missense_variant 0.88
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 1.0
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247678 c.1166delT frameshift_variant 0.12
embB 4247685 p.Leu391Trp missense_variant 0.13
embB 4249646 c.3136delG frameshift_variant 0.13
ubiA 4269365 p.Tyr157His missense_variant 0.12
aftB 4269372 c.-536G>T upstream_gene_variant 0.12
ethR 4326961 c.-588G>C upstream_gene_variant 0.11
ethR 4327712 p.Gly55Asp missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407945 c.258C>T synonymous_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0