TB-Profiler result

Run: SRR21677871
Summary

Run ID: SRR21677871

Sample name:

Date: 04-04-2023 02:49:05

Number of reads: 334476

Percentage reads mapped: 98.9

Strain: lineage4.1.1

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
katG 2156070 c.41delG frameshift_variant 0.13 isoniazid
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 5491 c.252T>C synonymous_variant 0.12
gyrB 6077 p.Gly280Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490985 c.204delG frameshift_variant 0.12
ccsA 620383 p.Pro165Thr missense_variant 0.12
rpoB 759619 c.-188C>T upstream_gene_variant 0.15
rpoB 759679 c.-127_-126delGC upstream_gene_variant 0.25
rpoB 760585 p.Asn260Ser missense_variant 0.11
rpoB 760798 p.Asp331Gly missense_variant 0.14
rpoB 760847 c.1041C>G synonymous_variant 0.13
rpoB 761753 c.1947C>G synonymous_variant 0.12
rpoB 761818 p.Arg671Pro missense_variant 0.22
rpoC 763789 c.420C>T synonymous_variant 0.14
rpoC 764391 c.1023delC frameshift_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765860 p.Phe831Leu missense_variant 0.18
rpoC 766070 c.2701C>T synonymous_variant 1.0
rpoC 766314 p.Ser982Phe missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776551 p.Thr644Ala missense_variant 0.11
mmpL5 777279 p.Ala401Val missense_variant 0.11
mmpL5 779169 c.-689C>T upstream_gene_variant 0.25
mmpS5 779520 c.-615C>G upstream_gene_variant 0.12
mmpS5 779582 c.-677C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800728 c.-81C>A upstream_gene_variant 0.15
fbiC 1304156 p.Arg409Gln missense_variant 0.17
Rv1258c 1406329 p.Thr338Ser missense_variant 0.11
Rv1258c 1406366 c.975C>T synonymous_variant 0.15
Rv1258c 1406407 p.Pro312Ser missense_variant 0.11
Rv1258c 1407099 p.Leu81Arg missense_variant 0.4
embR 1416517 c.831C>G synonymous_variant 0.17
atpE 1460892 c.-153A>G upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474055 n.398C>T non_coding_transcript_exon_variant 0.12
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.25
rrl 1475016 n.1365_1367dupTGG non_coding_transcript_exon_variant 0.25
rpsA 1833474 c.-68C>T upstream_gene_variant 0.11
rpsA 1833702 p.Asp54Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918379 c.443_445delTCG disruptive_inframe_deletion 0.29
ndh 2102206 c.837G>C synonymous_variant 0.12
ndh 2102649 p.Ala132Ser missense_variant 0.14
ndh 2103171 c.-129G>A upstream_gene_variant 0.22
katG 2154078 p.Tyr678* stop_gained 0.11
katG 2154203 p.Asn637Tyr missense_variant 0.11
PPE35 2167880 p.Asn911Lys missense_variant 0.14
PPE35 2168020 p.Thr865Ala missense_variant 0.14
PPE35 2168598 c.2014dupG frameshift_variant 0.17
PPE35 2168703 p.Gly637Val missense_variant 0.33
PPE35 2169179 c.1434C>A synonymous_variant 0.11
PPE35 2169751 p.Gly288Arg missense_variant 0.12
PPE35 2170238 c.375T>C synonymous_variant 0.18
PPE35 2170291 p.Ala108Thr missense_variant 0.22
Rv1979c 2222542 p.Leu208Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290119 c.-878T>C upstream_gene_variant 0.12
eis 2714362 p.Ser324Cys missense_variant 0.14
eis 2715235 p.Ala33Val missense_variant 0.17
ahpC 2726445 p.Val85Phe missense_variant 0.11
pepQ 2859816 c.603G>C synonymous_variant 0.12
pepQ 2860068 p.Lys117Asn missense_variant 0.18
pepQ 2860122 p.Ser99Arg missense_variant 0.14
Rv2752c 3065266 p.Gly309Asp missense_variant 0.22
Rv2752c 3066244 c.-53G>T upstream_gene_variant 0.25
thyX 3067890 p.Ala19Val missense_variant 0.17
thyA 3074474 c.-3A>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086803 c.-17T>A upstream_gene_variant 0.11
ald 3086906 c.89dupG frameshift_variant 0.17
ald 3087454 p.Cys212Ser missense_variant 0.18
fbiD 3339541 p.Asp142Tyr missense_variant 0.15
Rv3083 3449201 c.700delC frameshift_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474367 p.Gly121Cys missense_variant 0.17
fprA 3474682 p.Asp226Asn missense_variant 0.13
fprA 3474790 p.Pro262Thr missense_variant 0.2
Rv3236c 3612039 p.Phe360Ile missense_variant 0.18
Rv3236c 3612940 c.177T>C synonymous_variant 0.11
Rv3236c 3612945 p.Ile58Val missense_variant 0.11
fbiA 3640416 c.-127G>T upstream_gene_variant 0.13
fbiB 3640617 c.-918G>A upstream_gene_variant 0.29
fbiA 3640834 p.Gln98* stop_gained 0.18
fbiA 3640955 p.Pro138Leu missense_variant 0.17
fbiA 3641124 c.585_587delTGC disruptive_inframe_deletion 0.17
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiB 3642552 c.1019delT frameshift_variant 0.18
fbiB 3642769 p.Leu412Pro missense_variant 0.13
alr 3840514 p.Arg303Ser missense_variant 0.13
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3877933 p.Leu192Arg missense_variant 0.22
rpoA 3878162 p.Val116Ile missense_variant 0.2
rpoA 3878367 c.141C>T synonymous_variant 0.12
ddn 3987113 c.270C>G synonymous_variant 0.17
clpC1 4038864 p.Val614Ala missense_variant 0.12
panD 4043975 p.Pro103Thr missense_variant 0.14
panD 4044275 p.Arg3Trp missense_variant 0.29
panD 4044388 c.-108delT upstream_gene_variant 0.25
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241095 c.1233C>T synonymous_variant 0.13
embC 4241440 p.Ser526Arg missense_variant 0.11
embC 4241550 p.Gly563Val missense_variant 0.11
embC 4242183 p.Ala774Val missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243337 c.105G>C synonymous_variant 0.12
embA 4243484 c.252C>A synonymous_variant 0.12
embA 4243514 c.282G>A synonymous_variant 0.14
embB 4245740 c.-774T>C upstream_gene_variant 0.15
embB 4247435 p.Arg308* stop_gained 0.29
embB 4247606 c.1093C>T synonymous_variant 0.18
embB 4249285 p.Glu924Asp missense_variant 0.13
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267771 c.1066T>C synonymous_variant 0.15
ubiA 4268961 p.Trp291Cys missense_variant 0.12
ubiA 4269649 p.Phe62Tyr missense_variant 0.11
ubiA 4269722 p.Ala38Ser missense_variant 0.11
ethA 4326694 p.Met260Ile missense_variant 0.22
ethR 4327021 c.-528G>A upstream_gene_variant 1.0
ethR 4328033 p.Ala162Glu missense_variant 0.14
ethR 4328102 c.555_560delGTCATT disruptive_inframe_deletion 0.17
ethR 4328111 p.Ala188Gly missense_variant 0.17
ethR 4328113 c.565_566insAATGAC stop_gained&disruptive_inframe_insertion 0.17
ethA 4328438 c.-965C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0