TB-Profiler result

Run: SRR6896171
Summary

Run ID: SRR6896171

Sample name:

Date: 04-04-2023 17:57:35

Number of reads: 198586

Percentage reads mapped: 99.51

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
rpoB 761196 p.Leu464Met missense_variant 1.0 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 5348 p.Thr37Ala missense_variant 0.14
gyrB 5394 p.Asn52Ser missense_variant 0.11
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5620 c.381G>C synonymous_variant 0.1
gyrB 5832 p.Ala198Gly missense_variant 0.12
gyrB 6010 c.771G>T synonymous_variant 0.15
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8214 p.Gln305Lys missense_variant 0.29
gyrA 8631 p.Ala444Ser missense_variant 0.13
gyrA 9043 p.Ala581Val missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9385 p.Arg695His missense_variant 0.4
gyrA 9554 c.2253G>A synonymous_variant 0.4
fgd1 491203 p.Gln141Lys missense_variant 0.33
mshA 575249 c.-99G>T upstream_gene_variant 0.22
mshA 576549 p.Ala401Asp missense_variant 0.4
ccsA 620155 p.Gly89Trp missense_variant 0.17
ccsA 620371 p.Ala161Ser missense_variant 0.25
rpoB 759708 c.-99G>T upstream_gene_variant 0.2
rpoB 759742 c.-65G>T upstream_gene_variant 0.2
rpoB 759786 c.-21G>T upstream_gene_variant 0.17
rpoB 761996 c.2190C>A synonymous_variant 0.33
rpoB 762638 p.Lys944Asn missense_variant 0.33
rpoB 763219 p.Ala1138Glu missense_variant 0.25
rpoC 764360 p.Asp331Tyr missense_variant 0.15
rpoC 764530 c.1161C>T synonymous_variant 0.22
rpoC 764539 c.1170C>A synonymous_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766087 c.2718C>A synonymous_variant 0.25
rpoC 766203 p.Gly945Val missense_variant 0.18
rpoC 766309 c.2940G>A synonymous_variant 0.33
rpoC 766682 p.Val1105Ile missense_variant 0.4
rpoC 766952 p.Ala1195Ser missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775660 p.Gln941* stop_gained 0.5
mmpL5 776222 c.2258delG frameshift_variant 0.5
mmpL5 777202 p.Ala427Thr missense_variant 0.25
mmpL5 777277 p.Leu402Ile missense_variant 0.33
mmpL5 777306 p.Pro392His missense_variant 0.29
mmpL5 777527 c.954G>A synonymous_variant 0.2
mmpL5 777818 c.663G>T synonymous_variant 0.17
mmpL5 777885 p.Ala199Val missense_variant 0.18
mmpL5 777919 p.Gly188Ser missense_variant 0.2
mmpL5 778183 p.Pro100Thr missense_variant 0.14
mmpR5 778379 c.-611C>T upstream_gene_variant 0.2
mmpS5 778940 c.-35C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781811 c.252C>A synonymous_variant 0.13
rplC 801418 p.Gly204* stop_gained 0.17
fbiC 1302862 c.-69C>T upstream_gene_variant 0.4
Rv1258c 1406120 c.1221C>A synonymous_variant 0.33
Rv1258c 1407353 c.-13A>G upstream_gene_variant 0.25
Rv1258c 1407539 c.-199C>A upstream_gene_variant 0.5
embR 1417153 c.195C>A synonymous_variant 0.18
embR 1417233 c.115C>T synonymous_variant 0.14
atpE 1461175 p.Glu44Ala missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472268 n.423G>C non_coding_transcript_exon_variant 0.15
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>T non_coding_transcript_exon_variant 0.17
rrs 1473294 n.1449A>T non_coding_transcript_exon_variant 0.12
rrl 1473997 n.340T>A non_coding_transcript_exon_variant 0.29
rrl 1474013 n.356A>T non_coding_transcript_exon_variant 0.25
rrl 1474627 n.970G>T non_coding_transcript_exon_variant 0.2
rrl 1475800 n.2143C>T non_coding_transcript_exon_variant 0.22
rrl 1475889 n.2232C>A non_coding_transcript_exon_variant 0.18
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.17
rrl 1476596 n.2939C>A non_coding_transcript_exon_variant 0.15
inhA 1674360 c.159G>T synonymous_variant 0.22
rpsA 1833439 c.-103G>A upstream_gene_variant 0.22
rpsA 1833599 p.Glu20* stop_gained 0.17
rpsA 1833880 p.Trp113Cys missense_variant 0.22
rpsA 1833950 p.Gly137Cys missense_variant 0.17
rpsA 1834238 p.Gly233Cys missense_variant 0.17
rpsA 1834762 c.1221C>T synonymous_variant 0.17
rpsA 1834975 c.1434C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918593 c.654G>T synonymous_variant 0.5
ndh 2102571 p.Ala158Ser missense_variant 0.15
ndh 2102711 p.Pro111Leu missense_variant 0.22
ndh 2103133 c.-91G>A upstream_gene_variant 0.29
katG 2155455 c.657G>A synonymous_variant 0.4
katG 2155859 p.Thr85Ala missense_variant 0.18
PPE35 2167712 c.2901C>A synonymous_variant 0.25
PPE35 2168129 c.2484G>T synonymous_variant 0.25
PPE35 2168330 c.2283G>T synonymous_variant 0.29
PPE35 2169101 c.1512G>T synonymous_variant 0.25
PPE35 2169742 c.870delG frameshift_variant 0.25
Rv1979c 2222692 p.Ala158Val missense_variant 0.2
Rv1979c 2223016 p.Ala50Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714347 p.Phe329Tyr missense_variant 0.25
eis 2715176 p.Gly53Ser missense_variant 0.18
eis 2715218 p.Leu39Met missense_variant 0.17
eis 2715244 p.Pro30His missense_variant 0.22
ahpC 2725918 c.-274delA upstream_gene_variant 0.33
ahpC 2725930 c.-263C>A upstream_gene_variant 0.25
ahpC 2725938 c.-255G>A upstream_gene_variant 0.22
ahpC 2725978 c.-215G>A upstream_gene_variant 0.2
ahpC 2726252 c.60C>T synonymous_variant 0.5
ahpC 2726710 p.Leu173Pro missense_variant 0.12
folC 2746290 p.Arg437Ser missense_variant 0.17
folC 2747316 c.283C>A synonymous_variant 0.5
folC 2747404 c.195G>A synonymous_variant 0.4
pepQ 2859835 p.Ala195Val missense_variant 0.13
pepQ 2859839 p.Val194Met missense_variant 0.12
pepQ 2860494 c.-76T>A upstream_gene_variant 0.33
Rv2752c 3064952 p.Gly414Ser missense_variant 0.2
Rv2752c 3065473 p.Ser240Tyr missense_variant 0.5
Rv2752c 3065739 c.453G>A synonymous_variant 0.2
Rv2752c 3065799 c.393C>A synonymous_variant 0.38
thyX 3067899 p.Asp16Ala missense_variant 0.25
thyX 3068118 c.-173C>T upstream_gene_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073901 p.Gln191* stop_gained 0.15
thyA 3074130 c.342G>T synonymous_variant 0.17
thyA 3074245 p.Gly76Glu missense_variant 0.29
thyA 3074409 c.63C>A synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087630 p.Gln271* stop_gained 0.33
fbiD 3339591 c.474G>T synonymous_variant 0.29
fbiD 3339596 p.Pro160Gln missense_variant 0.29
fbiD 3339700 p.Leu195Val missense_variant 0.29
Rv3083 3448353 c.-151T>C upstream_gene_variant 0.18
Rv3083 3448626 c.123G>T synonymous_variant 0.25
Rv3083 3448758 c.255C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474778 p.Arg258Cys missense_variant 0.17
whiB7 3568683 c.-4G>T upstream_gene_variant 0.4
Rv3236c 3612225 p.Ala298Thr missense_variant 0.25
fbiB 3641545 p.Pro4His missense_variant 0.2
fbiB 3642129 p.Ala199Ser missense_variant 0.33
fbiB 3642376 p.Ala281Val missense_variant 0.5
alr 3840206 c.1215T>C synonymous_variant 0.12
alr 3840462 p.Arg320Gln missense_variant 0.2
alr 3841272 p.Arg50Leu missense_variant 0.14
rpoA 3877995 c.513G>A synonymous_variant 0.17
rpoA 3878043 c.465G>T synonymous_variant 0.18
rpoA 3878093 p.Val139Ile missense_variant 0.13
ddn 3986777 c.-67C>T upstream_gene_variant 0.2
ddn 3986946 p.Glu35* stop_gained 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038439 p.Lys756Glu missense_variant 0.18
clpC1 4038551 c.2154C>G synonymous_variant 0.12
clpC1 4039063 p.Ser548Ala missense_variant 0.17
clpC1 4039673 c.1032G>T synonymous_variant 0.15
clpC1 4040743 c.-47_-40delGGTGTCGA upstream_gene_variant 0.33
panD 4043989 p.Ala98Asp missense_variant 0.25
embC 4239895 c.33C>A synonymous_variant 0.29
embC 4240941 p.Ser360Ile missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242777 p.Gln972Arg missense_variant 0.18
embC 4243137 p.Arg1092Leu missense_variant 0.22
embB 4247107 c.594C>T synonymous_variant 0.22
embB 4247625 p.Pro371Leu missense_variant 0.33
embB 4247659 c.1146C>A synonymous_variant 0.33
embB 4247856 p.Gly448Asp missense_variant 0.33
embB 4248349 c.1836G>A synonymous_variant 0.2
embB 4248460 c.1947C>A synonymous_variant 0.18
embB 4249196 p.Gly895Trp missense_variant 0.14
aftB 4267171 p.Gln556* stop_gained 0.2
aftB 4267665 p.Asn391Ser missense_variant 0.15
aftB 4268027 p.Leu270Phe missense_variant 0.25
aftB 4269618 c.-782C>A upstream_gene_variant 0.5
ubiA 4269863 c.-30C>A upstream_gene_variant 0.14
ubiA 4269893 c.-60G>T upstream_gene_variant 0.18
ethA 4326529 c.945C>T synonymous_variant 0.25
ethA 4326606 p.Asp290Tyr missense_variant 0.25
whiB6 4338477 p.Phe15Leu missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407550 p.Met218Lys missense_variant 0.33
gid 4407710 p.Glu165Lys missense_variant 0.29
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408241 c.-39G>A upstream_gene_variant 0.17
gid 4408262 c.-60A>G upstream_gene_variant 0.17