TB-Profiler result

Run: ERR2228819
Summary

Run ID: ERR2228819

Sample name:

Date: 31-03-2023 16:22:01

Number of reads: 610402

Percentage reads mapped: 99.2

Strain: lineage4.8

Drug-resistance: RR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.98
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
rpoB 761136 p.Thr444Pro missense_variant 0.2 rifampicin
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 6210 p.Leu324Gln missense_variant 0.22
gyrB 6456 p.Val406Asp missense_variant 0.25
gyrB 6571 p.Asp444Glu missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8060 p.Met253Ile missense_variant 0.22
gyrA 8749 p.Leu483His missense_variant 0.25
fgd1 490590 c.-193A>C upstream_gene_variant 0.35
fgd1 491610 c.828A>T synonymous_variant 0.33
ccsA 620090 p.Gln67Leu missense_variant 0.17
ccsA 620492 p.Ser201Leu missense_variant 0.25
rpoB 759898 p.Asn31Thr missense_variant 0.5
rpoB 760841 c.1035T>G synonymous_variant 0.38
rpoB 761914 p.Asp703Ala missense_variant 0.18
rpoC 763367 c.-3T>A upstream_gene_variant 0.22
rpoC 763592 p.Cys75Ser missense_variant 0.27
rpoC 764915 p.Leu516Met missense_variant 0.22
rpoC 765495 p.Val709Gly missense_variant 0.29
rpoC 766432 c.3063T>A synonymous_variant 0.27
rpoC 766686 p.Glu1106Val missense_variant 0.29
mmpL5 775586 c.2895A>C stop_lost&splice_region_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 0.95
mmpL5 776569 p.Met638Leu missense_variant 0.25
mmpL5 777250 p.Tyr411Asp missense_variant 0.25
mmpL5 778144 p.Ile113Leu missense_variant 0.3
mmpS5 778543 p.Glu121Asp missense_variant 0.25
mmpL5 779100 c.-620A>C upstream_gene_variant 0.22
mmpR5 779266 p.Phe93Ile missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781592 c.33T>G synonymous_variant 0.5
rplC 800822 p.Gly5Asp missense_variant 0.17
rplC 801068 p.Asp87Ala missense_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304011 p.Thr361Pro missense_variant 0.31
fbiC 1304646 c.1716T>G synonymous_variant 0.25
Rv1258c 1406255 c.1086G>A synonymous_variant 0.27
Rv1258c 1407039 p.Val101Gly missense_variant 0.31
Rv1258c 1407075 p.Val89Gly missense_variant 0.27
embR 1416323 p.Asn342Thr missense_variant 0.27
embR 1416372 p.Ser326Arg missense_variant 0.27
embR 1416949 p.Gln133His missense_variant 0.33
atpE 1461074 c.30C>A synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471750 n.-96A>G upstream_gene_variant 0.25
rrs 1471801 n.-45A>T upstream_gene_variant 0.43
rrs 1471881 n.36A>T non_coding_transcript_exon_variant 0.4
rrs 1472549 n.704G>T non_coding_transcript_exon_variant 0.13
rrs 1472974 n.1129A>T non_coding_transcript_exon_variant 0.21
rrl 1473563 n.-95T>G upstream_gene_variant 0.33
rrl 1473822 n.165A>T non_coding_transcript_exon_variant 0.33
rrl 1473826 n.169A>T non_coding_transcript_exon_variant 0.67
rrl 1473844 n.187C>A non_coding_transcript_exon_variant 0.29
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474041 n.384T>C non_coding_transcript_exon_variant 0.25
rrl 1474161 n.504A>C non_coding_transcript_exon_variant 0.2
rrl 1475628 n.1971G>T non_coding_transcript_exon_variant 0.27
fabG1 1673154 c.-286A>C upstream_gene_variant 0.25
rpsA 1833543 c.2T>A start_lost 0.25
rpsA 1834026 p.Gln162Pro missense_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102559 p.Ser162Gly missense_variant 0.25
PPE35 2167814 c.2799C>T synonymous_variant 0.2
PPE35 2167846 p.Ser923Cys missense_variant 0.22
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169013 p.Val534Leu missense_variant 0.25
PPE35 2169226 p.Pro463Ala missense_variant 0.12
PPE35 2169278 c.1335T>G synonymous_variant 0.18
PPE35 2169329 p.Asn428Lys missense_variant 0.21
PPE35 2169798 p.Leu272Gln missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>G upstream_gene_variant 0.27
pncA 2289994 c.-753A>T upstream_gene_variant 0.29
pncA 2290023 c.-782A>G upstream_gene_variant 0.67
kasA 2518610 p.Thr166Pro missense_variant 0.25
eis 2715098 p.Thr79Pro missense_variant 0.4
folC 2747316 p.Arg95* stop_gained 0.2
folC 2747457 p.Thr48Pro missense_variant 0.2
pepQ 2859528 c.891T>C synonymous_variant 0.23
pepQ 2860114 p.Val102Gly missense_variant 0.25
ribD 2987069 c.231T>A synonymous_variant 0.43
Rv2752c 3064912 p.Val427Asp missense_variant 0.29
Rv2752c 3065098 p.Asn365Thr missense_variant 0.22
thyX 3067509 p.Leu146Gln missense_variant 0.2
thyX 3067651 p.Phe99Leu missense_variant 0.17
thyX 3067713 p.Val78Ala missense_variant 0.15
thyA 3073699 p.Lys258Ile missense_variant 0.18
thyA 3073828 p.Gln215Arg missense_variant 0.1
thyA 3074248 p.His75Leu missense_variant 0.2
thyA 3074365 p.Tyr36Phe missense_variant 0.27
Rv3236c 3612166 c.951A>T synonymous_variant 0.29
Rv3236c 3612377 p.Val247Ala missense_variant 0.33
Rv3236c 3613146 c.-30T>G upstream_gene_variant 0.17
fbiA 3640968 p.Leu142Phe missense_variant 0.4
fbiB 3642340 p.Asp269Ala missense_variant 0.4
alr 3840878 p.Gln181His missense_variant 0.18
clpC1 4039691 c.1014G>C synonymous_variant 0.21
clpC1 4040031 p.Val225Gly missense_variant 0.14
clpC1 4040249 p.Glu152Asp missense_variant 0.43
clpC1 4040574 p.Val44Gly missense_variant 0.38
clpC1 4040593 p.Ile38Val missense_variant 0.2
panD 4043998 p.Asp95Ala missense_variant 0.27
embC 4242002 p.Leu714Val missense_variant 0.29
embC 4242069 p.Val736Gly missense_variant 0.21
embC 4242319 p.Glu819Asp missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242908 p.Phe1016Val missense_variant 0.2
embA 4243365 p.Trp45Arg missense_variant 0.2
embA 4243546 p.Leu105Arg missense_variant 0.18
embA 4245726 p.Leu832Met missense_variant 0.5
embB 4246743 p.Val77Gly missense_variant 0.17
aftB 4267596 p.Tyr414Ser missense_variant 0.15
aftB 4268034 p.Val268Ala missense_variant 0.5
ethA 4327176 p.Phe100Leu missense_variant 0.4
ethR 4327207 c.-342C>A upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407553 p.Arg217Gln missense_variant 0.2
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0