TB-Profiler result

Run: SRR21677862
Summary

Run ID: SRR21677862

Sample name:

Date: 04-04-2023 02:48:44

Number of reads: 443462

Percentage reads mapped: 99.6

Strain: lineage4

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
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
pncA 2288775 c.460_466delAGGGTGC frameshift_variant 0.13 pyrazinamide
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 5770 c.531C>A synonymous_variant 0.11
gyrB 5800 c.562delG frameshift_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7812 p.Pro171Ser missense_variant 0.12
gyrA 9563 p.Met754Ile missense_variant 0.12
gyrA 9617 p.Ser772Arg missense_variant 0.14
fgd1 490703 c.-80C>T upstream_gene_variant 0.18
fgd1 491705 p.Leu308Gln missense_variant 0.12
mshA 575292 c.-56C>T upstream_gene_variant 0.2
mshA 575403 p.Val19Ala missense_variant 0.22
mshA 575792 p.Asp149Tyr missense_variant 0.17
mshA 575966 p.Val207Phe missense_variant 0.13
mshA 576408 p.Ser354Leu missense_variant 0.17
ccsA 620063 p.Ser58Ile missense_variant 0.18
rpoB 761196 c.1390C>T synonymous_variant 0.13
rpoB 761243 c.1437G>T synonymous_variant 0.18
rpoC 763253 c.-117G>A upstream_gene_variant 0.15
rpoC 763936 c.567C>A synonymous_variant 0.17
rpoC 764268 p.Ala300Glu missense_variant 0.13
rpoC 764505 p.Asp379Val missense_variant 0.12
rpoC 764604 p.Arg412Leu missense_variant 0.17
rpoC 765643 p.Lys758Asn missense_variant 0.13
rpoC 765871 c.2504delC frameshift_variant 0.12
rpoC 766143 c.2777delG frameshift_variant 0.18
rpoC 766370 p.Gln1001Lys missense_variant 0.2
rpoC 767300 p.Gly1311Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775928 p.Asn851Lys missense_variant 0.29
mmpL5 776204 c.2277C>A synonymous_variant 0.12
mmpL5 778470 p.Gln4Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801205 p.Arg133Ser missense_variant 0.13
fbiC 1304225 p.Gly432Asp missense_variant 0.67
fbiC 1304818 p.Val630Leu missense_variant 0.11
fbiC 1304869 p.Leu647Met missense_variant 0.13
fbiC 1304982 p.Lys684Asn missense_variant 0.22
fbiC 1305037 c.2107C>A synonymous_variant 0.25
Rv1258c 1406102 c.1239G>T synonymous_variant 0.17
embR 1416422 p.Arg309Gln missense_variant 0.25
embR 1416887 p.Arg154His missense_variant 0.12
embR 1417486 c.-139G>A upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
inhA 1674069 c.-133G>T upstream_gene_variant 0.12
inhA 1674448 p.Gly83Arg missense_variant 0.12
inhA 1674498 c.297G>A synonymous_variant 0.11
inhA 1674737 p.Ala179Val missense_variant 0.14
rpsA 1834505 p.His322Ile missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918014 c.75G>A synonymous_variant 0.2
tlyA 1918036 p.Arg33Ser missense_variant 0.2
tlyA 1918291 p.Leu118Met missense_variant 0.11
ndh 2101680 p.Ser455Thr missense_variant 0.17
ndh 2101746 p.Asp433Asn missense_variant 0.12
ndh 2102124 p.Pro307Thr missense_variant 0.12
ndh 2102368 c.675C>A synonymous_variant 0.14
katG 2154008 p.Ser702Pro missense_variant 0.14
katG 2155240 p.Ala291Asp missense_variant 0.15
katG 2155249 p.Pro288His missense_variant 0.15
katG 2155258 p.Gly285Val missense_variant 0.17
PPE35 2167828 p.Ala929Ser missense_variant 0.18
PPE35 2168059 p.Gln852* stop_gained 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169266 c.1347C>A synonymous_variant 0.13
PPE35 2170155 p.Ala153Asp missense_variant 0.13
PPE35 2170222 p.Pro131Thr missense_variant 0.2
PPE35 2170372 p.Thr81Ala missense_variant 0.18
PPE35 2170376 c.237G>A synonymous_variant 0.18
PPE35 2170499 c.114A>G synonymous_variant 0.15
PPE35 2170505 c.108C>G synonymous_variant 0.15
PPE35 2170508 c.105A>C synonymous_variant 0.15
PPE35 2170532 c.81G>C synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223303 c.-139G>A upstream_gene_variant 0.12
pncA 2289093 p.Phe50Ser missense_variant 0.5
pncA 2289386 c.-145A>G upstream_gene_variant 0.12
pncA 2289683 c.-442C>A upstream_gene_variant 0.17
pncA 2290128 c.-887T>C upstream_gene_variant 0.1
kasA 2518269 p.Thr52Asn missense_variant 0.11
kasA 2518332 p.Gly73Ala missense_variant 0.12
kasA 2518569 p.Ala152Glu missense_variant 0.2
kasA 2518646 p.Ile178Val missense_variant 0.13
kasA 2518795 c.681C>T synonymous_variant 0.18
kasA 2519078 p.Glu322* stop_gained 0.12
eis 2715457 c.-125T>C upstream_gene_variant 0.14
ahpC 2725966 c.-227C>T upstream_gene_variant 0.12
ahpC 2725974 c.-219C>A upstream_gene_variant 0.11
ahpC 2726123 c.-70G>T upstream_gene_variant 0.15
ahpC 2726169 c.-24T>C upstream_gene_variant 0.22
folC 2746451 p.Gly383Val missense_variant 0.14
folC 2746531 c.1068G>T synonymous_variant 0.12
folC 2747012 p.Pro196Leu missense_variant 0.12
pepQ 2859501 c.918G>T synonymous_variant 0.12
pepQ 2860222 p.Ser66* stop_gained 0.22
ribD 2987207 c.369C>A synonymous_variant 0.18
ribD 2987348 c.510G>T synonymous_variant 0.17
ribD 2987457 p.Val207Met missense_variant 0.14
Rv2752c 3064581 c.1611C>T synonymous_variant 0.12
Rv2752c 3064635 c.1557G>T synonymous_variant 0.12
thyX 3067388 c.558C>T synonymous_variant 0.12
thyX 3067688 c.258G>T synonymous_variant 0.14
thyX 3067717 p.Ser77Cys missense_variant 0.13
thyX 3067873 p.Trp25Arg missense_variant 0.12
thyX 3068127 c.-182G>A upstream_gene_variant 0.11
thyA 3073820 p.Leu218Met missense_variant 0.11
ald 3087150 p.Gly111Arg missense_variant 0.12
ald 3087767 c.948G>T synonymous_variant 0.15
fbiD 3339324 c.207G>A synonymous_variant 0.25
fprA 3474043 p.Pro13Thr missense_variant 0.17
fprA 3474779 p.Arg258His missense_variant 0.11
fprA 3475091 p.Arg362Leu missense_variant 0.12
Rv3236c 3612006 p.Arg371Gly missense_variant 0.12
Rv3236c 3612356 c.760delG frameshift_variant 0.25
fbiA 3641387 p.Thr282Ile missense_variant 0.12
fbiB 3641708 c.174C>A synonymous_variant 0.33
fbiB 3642693 p.Ala387Ser missense_variant 0.12
fbiB 3642715 p.Gly394Val missense_variant 0.11
alr 3841214 c.207C>T synonymous_variant 0.22
alr 3841477 c.-57G>A upstream_gene_variant 0.17
rpoA 3878257 p.Val84Ala missense_variant 0.11
ddn 3986940 p.Asp33Tyr missense_variant 0.15
clpC1 4038177 p.Pro843Arg missense_variant 0.12
clpC1 4038815 c.1890G>T synonymous_variant 0.17
clpC1 4039134 p.Ala524Asp missense_variant 0.12
clpC1 4039153 p.Ile518Phe missense_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039883 p.Lys274Asn missense_variant 0.11
clpC1 4040483 c.222G>T synonymous_variant 0.22
clpC1 4040486 c.219G>T synonymous_variant 0.18
clpC1 4040599 p.Gly36Cys missense_variant 0.11
panD 4044149 p.Thr45Ala missense_variant 0.2
panD 4044255 p.Lys9Asn missense_variant 0.2
panD 4044452 c.-171C>A upstream_gene_variant 0.12
panD 4044465 c.-186_-185delCT upstream_gene_variant 0.12
embC 4240032 p.Ala57Gly missense_variant 0.12
embC 4240834 c.972C>T synonymous_variant 0.14
embC 4241007 p.Ala382Val missense_variant 0.18
embC 4242515 p.Val885Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242662 c.2802dupC frameshift_variant 0.14
embA 4242952 c.-281T>A upstream_gene_variant 0.12
embA 4243485 p.Asn85Tyr missense_variant 0.12
embA 4243990 p.Ala253Val missense_variant 0.14
embA 4244517 p.Leu429Met missense_variant 0.11
embB 4246542 p.Ser10Asn missense_variant 0.17
embB 4246760 p.Val83Leu missense_variant 0.15
embB 4247447 p.His312Tyr missense_variant 0.22
embB 4247840 p.Gly443Cys missense_variant 0.14
embB 4249070 p.Gln853Lys missense_variant 0.14
embB 4249753 p.Leu1080Phe missense_variant 0.15
aftB 4267669 p.Ala390Ser missense_variant 0.17
aftB 4267869 p.Ala323Gly missense_variant 0.13
aftB 4268026 p.Val271Met missense_variant 0.12
aftB 4269576 c.-740C>T upstream_gene_variant 0.14
ubiA 4269718 p.Ala39Glu missense_variant 0.15
ubiA 4269730 p.Ala35Glu missense_variant 0.15
ethA 4326520 c.954A>G synonymous_variant 0.12
ethA 4326704 p.Pro257Gln missense_variant 0.12
ethA 4327078 p.Glu132Asp missense_variant 0.13
ethA 4327518 c.-45G>T upstream_gene_variant 0.12
ethA 4328070 c.-597C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0