TB-Profiler result

Run: ERR1949963
Summary

Run ID: ERR1949963

Sample name:

Date: 31-03-2023 15:35:49

Number of reads: 571325

Percentage reads mapped: 99.27

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 5510 p.Ser91Thr missense_variant 0.2
gyrB 5770 c.531C>A synonymous_variant 0.2
gyrB 7083 p.Glu615Gly missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491012 p.Pro77His missense_variant 0.18
fgd1 491254 p.Lys158* stop_gained 0.29
fgd1 491570 p.Asp263Ala missense_variant 0.29
ccsA 619820 c.-71T>G upstream_gene_variant 0.29
ccsA 620078 p.Ile63Ser missense_variant 0.4
ccsA 620684 p.Glu265Gly missense_variant 0.15
rpoB 759914 c.108T>A synonymous_variant 0.4
rpoB 762182 c.2380delG frameshift_variant 0.2
rpoB 762320 c.2514C>A synonymous_variant 0.22
rpoB 762534 p.Ile910Phe missense_variant 0.22
rpoC 765563 p.Ser732Ala missense_variant 0.2
rpoC 765927 p.Thr853Asn missense_variant 0.25
rpoC 766865 p.Thr1166Pro missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776307 p.Asp725Ala missense_variant 0.33
mmpL5 776988 p.Pro498Leu missense_variant 0.33
mmpL5 777590 c.891G>A synonymous_variant 1.0
mmpL5 778141 p.Gly114Arg missense_variant 0.12
mmpL5 778919 c.-439A>T upstream_gene_variant 0.29
mmpR5 779015 p.Gln9Leu missense_variant 0.25
mmpL5 779100 c.-620A>C upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781587 p.Lys10* stop_gained 0.2
fbiC 1302894 c.-37T>G upstream_gene_variant 0.18
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.19
fbiC 1305033 c.2103T>G synonymous_variant 0.27
Rv1258c 1406622 p.Leu240Gln missense_variant 0.27
Rv1258c 1406759 p.Glu194Asp missense_variant 0.18
embR 1416345 p.Thr335Ala missense_variant 0.17
atpE 1460965 c.-80A>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473890 n.233T>A non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476401 n.2744T>G non_coding_transcript_exon_variant 0.25
rpsA 1833930 p.Val130Gly missense_variant 0.22
rpsA 1834121 p.Thr194Pro missense_variant 0.25
rpsA 1834425 p.Gln295Pro missense_variant 0.17
rpsA 1834947 p.Gln469Pro missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918532 p.Val198Gly missense_variant 0.31
tlyA 1918607 p.Val223Gly missense_variant 0.29
ndh 2102285 p.Asp253Ala missense_variant 0.29
katG 2154542 p.Ile524Leu missense_variant 0.22
katG 2156488 c.-377C>A upstream_gene_variant 0.18
PPE35 2167675 p.Leu980Met missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169515 c.1098T>A synonymous_variant 0.67
PPE35 2169900 p.Gly238Val missense_variant 0.29
PPE35 2169910 p.Asn235Tyr missense_variant 0.36
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.27
PPE35 2170528 p.Ser29Ala missense_variant 0.22
Rv1979c 2221905 c.1260T>C synonymous_variant 0.33
Rv1979c 2222160 c.1005T>G synonymous_variant 0.18
Rv1979c 2222453 p.Ile238Leu missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289420 c.-180delC upstream_gene_variant 0.29
eis 2715506 c.-174T>G upstream_gene_variant 0.12
ahpC 2726164 c.-29C>A upstream_gene_variant 0.33
folC 2746740 p.Ser287Pro missense_variant 0.22
pepQ 2859332 p.Thr363Pro missense_variant 0.22
pepQ 2859676 p.Glu248Val missense_variant 0.17
pepQ 2859704 p.Leu239Val missense_variant 0.22
pepQ 2860417 p.Val1Ala missense_variant 0.25
ribD 2986681 c.-158A>C upstream_gene_variant 0.25
ribD 2986713 c.-126A>T upstream_gene_variant 0.29
Rv2752c 3064618 p.Asp525Ala missense_variant 0.33
Rv2752c 3064967 p.Leu409Met missense_variant 0.18
Rv2752c 3065522 c.670C>A synonymous_variant 0.18
Rv2752c 3065914 p.Leu93Gln missense_variant 0.29
thyA 3073692 c.780A>T synonymous_variant 0.29
thyA 3074358 p.Leu38Phe missense_variant 0.33
ald 3087917 c.1098C>G synonymous_variant 0.2
fbiD 3339275 p.Val53Gly missense_variant 0.18
fprA 3473960 c.-47T>A upstream_gene_variant 0.25
fprA 3474763 p.Arg253Cys missense_variant 0.18
whiB7 3568652 p.Thr10Pro missense_variant 0.25
Rv3236c 3612844 c.273G>A synonymous_variant 0.25
Rv3236c 3613048 c.69A>T synonymous_variant 0.5
Rv3236c 3613261 c.-145T>A upstream_gene_variant 0.25
fbiA 3640763 p.Asp74Ala missense_variant 0.21
fbiA 3641182 p.Ser214Ala missense_variant 0.22
fbiB 3642015 p.Thr161Pro missense_variant 0.15
fbiB 3642299 p.Gln255His missense_variant 0.29
fbiB 3642404 p.His290Gln missense_variant 0.22
alr 3840952 p.Lys157* stop_gained 0.3
alr 3841365 p.Gly19Ala missense_variant 0.2
rpoA 3877696 p.Thr271Ile missense_variant 0.25
clpC1 4038929 c.1776G>T synonymous_variant 0.67
clpC1 4040209 p.Ser166Ala missense_variant 0.36
clpC1 4040388 p.Glu106Ala missense_variant 0.22
panD 4043911 p.Val124Glu missense_variant 0.44
embC 4241043 p.Asn394Thr missense_variant 0.19
embC 4241127 p.Leu422Arg missense_variant 0.67
embC 4241450 p.Ser530Ala missense_variant 0.25
embC 4241510 p.Met550Leu missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244780 c.1548C>A synonymous_variant 0.4
embA 4245510 p.Pro760Ser missense_variant 0.2
embA 4245927 p.Thr899Pro missense_variant 0.17
embB 4248357 p.Ser615Cys missense_variant 0.13
embB 4249282 c.2769A>G synonymous_variant 0.12
embB 4249547 p.Phe1012Ile missense_variant 0.18
embB 4249743 p.Gln1077Arg missense_variant 0.67
aftB 4267106 c.1731T>A synonymous_variant 0.29
aftB 4267113 p.Leu575Pro missense_variant 0.25
aftB 4268167 p.Tyr224His missense_variant 0.15
ethA 4326273 p.Phe401Val missense_variant 0.22
ethA 4326441 p.Asn345Asp missense_variant 0.25
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4327703 p.Lys52Met missense_variant 0.29
ethA 4327746 c.-273T>A upstream_gene_variant 0.29
ethR 4327894 p.Ser116Ala missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408309 c.-107A>C upstream_gene_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0