TB-Profiler result

Run: ERR2229186

Summary

Run ID: ERR2229186

Sample name:

Date: 31-03-2023 16:47:16

Number of reads: 712735

Percentage reads mapped: 99.16

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
gyrB 6232 c.993C>T synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8155 c.856delT frameshift_variant 0.17
gyrA 9782 c.2481C>T synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.31
mshA 576111 p.Ala255Gly missense_variant 0.36
ccsA 620123 p.Arg78Pro missense_variant 0.17
rpoB 761133 p.Leu443Val missense_variant 0.13
rpoB 761759 p.Tyr651* stop_gained 0.17
rpoB 761821 p.Ser672Phe missense_variant 0.2
rpoC 765078 p.Ser570Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775909 p.Leu858Phe missense_variant 0.17
mmpL5 775910 c.2571G>A synonymous_variant 0.17
mmpL5 775915 p.Ala856Ser missense_variant 0.17
mmpL5 775918 p.Val855Ile missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.29
mmpL5 777763 p.Leu240Met missense_variant 0.2
mmpL5 778910 c.-430G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303816 p.Arg296Gly missense_variant 0.2
fbiC 1303984 p.Asp352Asn missense_variant 0.18
embR 1417386 c.-39T>C upstream_gene_variant 0.12
atpE 1461244 c.202dupC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471881 n.36A>T non_coding_transcript_exon_variant 0.17
rrs 1472722 n.881delG non_coding_transcript_exon_variant 0.15
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475466 n.1809A>T non_coding_transcript_exon_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.25
fabG1 1673349 c.-91G>C upstream_gene_variant 0.23
fabG1 1673357 c.-83G>A upstream_gene_variant 0.26
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 0.51
rpsA 1833425 c.-117C>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102819 p.Val75Glu missense_variant 0.25
katG 2154325 p.Asn596Ser missense_variant 0.17
katG 2155191 c.921A>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.38
PPE35 2169091 p.Val508Leu missense_variant 0.22
PPE35 2169206 c.1407A>G synonymous_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
PPE35 2170159 p.Ala152Ser missense_variant 0.13
PPE35 2170164 p.Ala150Val missense_variant 0.13
PPE35 2170169 c.444A>G synonymous_variant 0.13
PPE35 2170175 p.Leu146Ile missense_variant 0.18
PPE35 2170178 c.435T>C synonymous_variant 0.14
PPE35 2170189 p.Glu142Gln missense_variant 0.13
PPE35 2170392 p.Gly74Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518904 c.790C>A synonymous_variant 0.12
kasA 2519014 p.Leu300Phe missense_variant 0.18
pepQ 2859448 p.Val324Thr missense_variant 0.13
pepQ 2859457 p.Val321Thr missense_variant 0.12
pepQ 2859601 p.Val273Gly missense_variant 0.18
ribD 2986872 p.Thr12Pro missense_variant 0.17
Rv2752c 3066367 c.-176G>A upstream_gene_variant 0.25
thyX 3067799 p.Lys49Asn missense_variant 0.18
thyA 3074518 c.-47G>A upstream_gene_variant 0.12
fbiD 3339364 p.Pro83Ala missense_variant 0.2
fbiD 3339749 p.Val211Ala missense_variant 0.29
whiB7 3568428 c.252A>G synonymous_variant 0.38
Rv3236c 3612509 p.Gly203Val missense_variant 0.25
Rv3236c 3612612 p.Phe169Ile missense_variant 0.15
Rv3236c 3613097 p.Leu7Arg missense_variant 0.29
alr 3840801 p.Ile207Thr missense_variant 0.12
alr 3840912 c.508delG frameshift_variant 0.13
alr 3841222 p.Ala67Pro missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877597 p.Leu304Pro missense_variant 0.11
ddn 3986680 c.-164C>A upstream_gene_variant 0.13
clpC1 4039161 p.His515Gly missense_variant 0.14
clpC1 4039169 p.Glu512Asp missense_variant 0.25
embC 4240156 p.Gln98His missense_variant 0.11
embC 4240551 p.Lys230Met missense_variant 0.13
embC 4241783 c.1923delG frameshift_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243256 c.24A>T synonymous_variant 0.14
embA 4245922 p.Gly897Asp missense_variant 0.2
embB 4246418 c.-96G>T upstream_gene_variant 0.14
embB 4246765 c.252G>A synonymous_variant 0.2
embB 4247028 p.Leu172Arg missense_variant 0.4
embB 4247470 c.957T>C synonymous_variant 0.14
embB 4247472 p.Phe320Tyr missense_variant 0.14
embB 4248233 p.Leu574Met missense_variant 0.15
ethR 4328111 p.Ala188Gly missense_variant 0.27
ethR 4328113 c.565_566insAATGAC stop_gained&disruptive_inframe_insertion 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0