TB-Profiler result

Run: SRR4033481
Summary

Run ID: SRR4033481

Sample name:

Date: 04-04-2023 06:07:29

Number of reads: 892860

Percentage reads mapped: 99.6

Strain: lineage4.3.2.1

Drug-resistance: Other

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 0.98
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gid 4407830 p.Gln125* stop_gained 0.15 streptomycin
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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5909 p.Ser224Cys missense_variant 0.18
gyrB 6049 c.810G>C synonymous_variant 0.11
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7342 p.Arg14Pro missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7648 p.Phe116Tyr missense_variant 0.18
gyrA 8376 p.Asp359Asn missense_variant 0.12
gyrA 8926 p.Lys542Arg missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9312 p.Leu671Val missense_variant 0.11
gyrA 9616 p.Ser772Thr missense_variant 0.14
gyrA 9705 p.Arg802Trp missense_variant 0.12
fgd1 490633 c.-149delA upstream_gene_variant 0.14
fgd1 491764 c.982C>T synonymous_variant 0.15
mshA 576542 p.Ala399Thr missense_variant 0.14
mshA 576754 c.1407C>T synonymous_variant 0.15
ccsA 619840 c.-51G>A upstream_gene_variant 0.14
rpoB 760513 p.Gly236Asp missense_variant 0.18
rpoB 761177 c.1371G>T synonymous_variant 0.17
rpoB 762106 p.Ile767Asn missense_variant 0.13
rpoB 763111 c.3308delG frameshift_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 0.96
rpoC 766456 c.3087C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776239 p.Gly748Arg missense_variant 0.15
mmpL5 776359 p.Phe708Ile missense_variant 0.17
mmpL5 777844 p.Thr213Ala missense_variant 0.13
mmpR5 779071 p.Glu28* stop_gained 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781401 c.-159T>A upstream_gene_variant 0.2
fbiC 1303458 c.528G>C synonymous_variant 0.2
fbiC 1304429 p.Arg500Gln missense_variant 0.14
Rv1258c 1406270 c.1071C>T synonymous_variant 0.13
Rv1258c 1406350 p.Ile331Phe missense_variant 0.17
Rv1258c 1406727 p.Pro205His missense_variant 0.18
Rv1258c 1406952 p.Glu130Val missense_variant 0.22
Rv1258c 1406967 p.Asp125Val missense_variant 0.2
Rv1258c 1407186 p.Met52Lys missense_variant 0.18
atpE 1461047 c.3G>A start_lost 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471696 n.-150T>C upstream_gene_variant 0.14
rrs 1472042 n.197T>A non_coding_transcript_exon_variant 0.12
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472891 n.1046A>G non_coding_transcript_exon_variant 0.13
rrs 1472968 n.1123C>T non_coding_transcript_exon_variant 0.15
rrl 1475268 n.1611T>A non_coding_transcript_exon_variant 0.17
rrl 1475788 n.2131C>G non_coding_transcript_exon_variant 0.17
rrl 1475793 n.2136T>A non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>G non_coding_transcript_exon_variant 0.18
inhA 1674337 c.136C>T synonymous_variant 0.2
inhA 1674346 p.Arg49Cys missense_variant 0.22
inhA 1674736 p.Ala179Thr missense_variant 0.14
inhA 1674744 c.543G>A synonymous_variant 0.15
rpsA 1833625 p.Lys28Asn missense_variant 0.14
rpsA 1833642 p.Asn34Ser missense_variant 0.14
rpsA 1834906 c.1365G>C synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918359 c.420A>T synonymous_variant 0.14
ndh 2101959 c.1083delA frameshift_variant 0.13
katG 2154469 p.Gly548Asp missense_variant 0.17
katG 2155082 p.Thr344Ala missense_variant 0.12
katG 2155664 p.Pro150Thr missense_variant 0.13
katG 2156104 p.Glu3Val missense_variant 0.13
katG 2156523 c.-412G>A upstream_gene_variant 0.18
PPE35 2167878 p.Ser912Thr missense_variant 0.12
PPE35 2168172 p.Ile814Thr missense_variant 0.11
PPE35 2168257 p.Leu786Met missense_variant 0.13
PPE35 2168650 p.Val655Met missense_variant 0.12
PPE35 2168828 c.1785G>C synonymous_variant 0.11
PPE35 2169261 p.Leu451Pro missense_variant 0.13
PPE35 2169607 p.Asn336Asp missense_variant 0.11
PPE35 2170049 c.563dupC frameshift_variant 0.5
Rv1979c 2222475 c.690C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288942 c.300C>A synonymous_variant 0.13
pncA 2289383 c.-142G>T upstream_gene_variant 0.14
pncA 2290039 c.-798C>T upstream_gene_variant 0.12
kasA 2518610 c.500delC frameshift_variant 0.17
kasA 2518739 p.Ala209Pro missense_variant 0.14
eis 2714339 p.Lys332Glu missense_variant 0.18
eis 2714774 p.Pro187Ala missense_variant 0.12
eis 2715230 p.Ala35Thr missense_variant 0.18
ahpC 2726040 c.-153G>A upstream_gene_variant 0.15
ahpC 2726774 c.582G>A synonymous_variant 0.22
folC 2747544 p.Pro19Ser missense_variant 0.17
Rv2752c 3064671 c.1521C>G synonymous_variant 0.11
Rv2752c 3065888 p.Val102Ile missense_variant 0.12
Rv2752c 3066315 c.-124C>T upstream_gene_variant 0.22
Rv2752c 3067126 c.-935C>T upstream_gene_variant 0.5
thyA 3073806 c.666C>G synonymous_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 0.83
thyA 3074326 p.Lys49Ile missense_variant 0.15
ald 3086757 c.-63G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087150 p.Gly111Ser missense_variant 0.14
ald 3087355 p.Ala179Asp missense_variant 0.15
ald 3087652 p.Ser278Leu missense_variant 0.14
Rv3083 3448524 c.21C>A synonymous_variant 0.14
Rv3083 3449895 p.Met464Ile missense_variant 0.17
Rv3083 3449911 p.Ala470Thr missense_variant 0.17
fprA 3473839 c.-168G>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474322 p.Ala106Thr missense_variant 0.25
whiB7 3568547 p.Ser45Gly missense_variant 0.15
whiB7 3568836 c.-157A>G upstream_gene_variant 0.2
Rv3236c 3612902 p.Ala72Val missense_variant 0.13
fbiA 3640497 c.-46G>A upstream_gene_variant 0.12
fbiA 3640757 p.Gly72Glu missense_variant 0.17
fbiA 3640771 p.Arg77Cys missense_variant 0.18
fbiB 3642506 p.Asp324Glu missense_variant 0.13
fbiB 3642670 p.Ala379Val missense_variant 0.14
alr 3840648 p.Tyr258Phe missense_variant 0.17
alr 3840752 c.669C>A synonymous_variant 0.17
alr 3841081 p.His114Tyr missense_variant 0.13
rpoA 3877683 c.825G>T synonymous_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 0.95
clpC1 4038920 p.Phe595Leu missense_variant 0.15
clpC1 4039108 c.1597C>A synonymous_variant 0.14
clpC1 4039115 c.1589_1590insT frameshift_variant 0.17
embC 4240043 p.Trp61Arg missense_variant 0.18
embC 4240286 p.Ala142Thr missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243137 p.Arg1092Leu missense_variant 0.15
embA 4243557 p.Ala109Thr missense_variant 0.13
embA 4243877 c.645G>T synonymous_variant 0.12
embA 4243989 p.Ala253Thr missense_variant 0.29
embA 4244163 p.Leu311Ile missense_variant 0.17
embA 4245801 p.Tyr857His missense_variant 0.13
embB 4245807 c.-707T>C upstream_gene_variant 0.17
embB 4247828 p.Ala439Thr missense_variant 0.13
embB 4248208 p.Ser565Arg missense_variant 0.12
embB 4248383 p.Asn624Asp missense_variant 0.12
embB 4248923 p.Met804Val missense_variant 0.11
embB 4249704 p.Leu1064Gln missense_variant 0.12
embB 4249714 c.3201C>T synonymous_variant 0.14
aftB 4268047 p.Tyr264His missense_variant 0.15
aftB 4268333 c.504C>T synonymous_variant 0.15
ethA 4326209 p.Pro422Arg missense_variant 0.13
ethA 4326496 c.978G>T synonymous_variant 0.2
ethA 4326539 p.Val312Ala missense_variant 0.14
whiB6 4338206 p.Val106Met missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.25
gid 4407620 p.Tyr195His missense_variant 0.17
gid 4407851 p.Arg118Cys missense_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408311 c.-109C>A upstream_gene_variant 0.15
gid 4408411 c.-209G>A upstream_gene_variant 0.15