TB-Profiler result

Run: SRR21677891
Summary

Run ID: SRR21677891

Sample name:

Date: 04-04-2023 02:49:37

Number of reads: 382725

Percentage reads mapped: 96.66

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;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
rpsL 781818 p.Val87Leu missense_variant 0.13 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 6090 p.Gly284Val missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7969 p.Val223Ala missense_variant 0.67
gyrA 8728 p.Arg476Leu missense_variant 0.5
gyrA 9028 p.Val576Ala missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9415 c.2115delC frameshift_variant 0.18
gyrA 9475 p.Val725Ala missense_variant 0.12
fgd1 490968 c.186C>T synonymous_variant 0.18
fgd1 491398 p.Lys206Glu missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
ccsA 620731 p.Ala281Ser missense_variant 0.15
rpoB 759772 c.-35C>A upstream_gene_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761094 p.Leu430Met missense_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.11
rpoB 761338 p.Arg511His missense_variant 0.22
rpoB 763016 p.Met1070Ile missense_variant 0.12
rpoB 763041 p.Leu1079Met missense_variant 0.17
rpoC 763843 c.474G>A synonymous_variant 0.12
rpoC 764019 p.Asp217Val missense_variant 0.13
rpoC 764073 p.Ile235Thr missense_variant 0.12
rpoC 764195 p.Ser276Thr missense_variant 0.13
rpoC 764436 p.Arg356Met missense_variant 0.18
rpoC 764842 c.1473C>A synonymous_variant 0.14
rpoC 765047 p.Leu560Met missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765670 c.2301C>T synonymous_variant 0.2
rpoC 765675 p.Glu769Val missense_variant 0.25
rpoC 766623 p.Arg1085Gln missense_variant 0.13
rpoC 766728 p.Glu1120Ala missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776906 p.Gln525His missense_variant 0.22
mmpL5 777128 c.1353A>G synonymous_variant 0.15
mmpL5 777131 c.1350C>T synonymous_variant 0.15
mmpL5 777136 p.Met449Leu missense_variant 0.12
mmpL5 777781 p.Thr234Ala missense_variant 0.2
mmpL5 777860 c.621C>A synonymous_variant 0.2
mmpL5 778450 p.Gly11Cys missense_variant 0.18
mmpL5 779112 c.-632G>T upstream_gene_variant 0.18
rpsL 781366 c.-194T>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781577 p.Gln6His missense_variant 0.11
rpsL 781663 p.Thr35Asn missense_variant 0.13
fbiC 1302954 c.24G>A synonymous_variant 0.2
fbiC 1302955 p.Ser9Thr missense_variant 0.2
fbiC 1303542 c.612C>A synonymous_variant 0.25
fbiC 1304826 c.1900delT frameshift_variant 0.14
fbiC 1304874 c.1944C>T synonymous_variant 0.15
fbiC 1305190 p.Ala754Ser missense_variant 0.11
embR 1416288 p.His354Asn missense_variant 0.12
embR 1417123 c.225C>T synonymous_variant 0.17
embR 1417464 c.-117C>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472428 n.583G>T non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.11
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.12
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.12
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.12
rrs 1473018 n.1173G>T non_coding_transcript_exon_variant 0.12
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.11
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.1
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.11
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.12
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.12
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.11
rrl 1473845 n.188G>T non_coding_transcript_exon_variant 0.14
rrl 1474383 n.726G>T non_coding_transcript_exon_variant 0.12
rrl 1475260 n.1603C>G non_coding_transcript_exon_variant 0.13
fabG1 1673151 c.-289C>A upstream_gene_variant 0.22
fabG1 1673261 c.-179C>A upstream_gene_variant 0.15
fabG1 1673806 p.Ala123Ser missense_variant 0.29
rpsA 1833521 c.-21T>A upstream_gene_variant 0.22
rpsA 1834521 p.Ala327Gly missense_variant 0.33
tlyA 1917903 c.-37G>A upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918498 p.Val187Leu missense_variant 0.14
ndh 2102147 p.Arg299Leu missense_variant 0.22
ndh 2102154 p.Leu297Ile missense_variant 0.22
ndh 2102199 p.Ala282Ser missense_variant 0.17
ndh 2102465 p.Ala193Val missense_variant 0.22
ndh 2103213 c.-171G>A upstream_gene_variant 1.0
katG 2154111 c.2001C>A synonymous_variant 0.2
katG 2154222 c.1890C>A synonymous_variant 0.25
katG 2154400 p.Arg571Leu missense_variant 0.15
katG 2154508 p.Asn535Ile missense_variant 0.12
katG 2155405 p.Asn236Ser missense_variant 0.17
katG 2155562 p.Gly184Cys missense_variant 0.12
katG 2155741 p.Gly124Asp missense_variant 0.11
katG 2156086 p.Thr9Ile missense_variant 0.11
PPE35 2168140 p.Ala825Thr missense_variant 0.18
PPE35 2168143 p.Phe824Leu missense_variant 0.18
PPE35 2168150 c.2463T>C synonymous_variant 0.25
PPE35 2168746 p.Gly623Arg missense_variant 1.0
PPE35 2169023 c.1590G>T synonymous_variant 0.25
PPE35 2169647 c.966C>T synonymous_variant 0.82
PPE35 2169970 p.Gly215Ser missense_variant 0.2
PPE35 2170556 c.56_57insA frameshift_variant 0.29
PPE35 2170613 c.-1G>A upstream_gene_variant 0.4
PPE35 2170683 c.-71A>G upstream_gene_variant 0.2
Rv1979c 2222259 c.906G>T synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223341 c.-177C>A upstream_gene_variant 0.12
pncA 2290209 c.-968A>T upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518169 p.Val19Phe missense_variant 0.17
kasA 2519044 c.930G>T synonymous_variant 0.2
ahpC 2726637 p.Ala149Thr missense_variant 0.14
folC 2746196 p.Ile468Asn missense_variant 0.14
folC 2746373 p.Pro409Leu missense_variant 0.12
pepQ 2859524 p.Gly299Cys missense_variant 0.17
pepQ 2859588 c.831G>A synonymous_variant 0.17
pepQ 2859898 p.Arg174Leu missense_variant 0.18
pepQ 2860491 c.-73C>T upstream_gene_variant 0.11
ribD 2987036 c.198C>A synonymous_variant 0.2
ribD 2987176 p.Glu113Gly missense_variant 0.15
Rv2752c 3064633 p.Ala520Val missense_variant 0.33
Rv2752c 3065151 c.1041G>A synonymous_variant 0.15
Rv2752c 3065618 p.Gly192Cys missense_variant 0.18
Rv2752c 3066152 p.Gly14Cys missense_variant 0.15
thyX 3067809 p.Ser46Ile missense_variant 0.29
thyA 3074283 p.Leu63Phe missense_variant 0.17
thyA 3074571 c.-100T>G upstream_gene_variant 0.13
ald 3086635 c.-185C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087425 p.Asp202Glu missense_variant 0.15
ald 3087465 p.His216Tyr missense_variant 0.12
ald 3087601 p.Gly261Asp missense_variant 0.4
fbiD 3339131 p.Pro5Leu missense_variant 0.17
Rv3083 3448306 c.-198G>A upstream_gene_variant 1.0
Rv3083 3448843 p.Cys114Ser missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475281 c.1275G>T synonymous_variant 0.25
whiB7 3568852 c.-173G>T upstream_gene_variant 0.14
Rv3236c 3612325 c.792T>C synonymous_variant 0.29
Rv3236c 3612587 p.Ser177Asn missense_variant 0.2
Rv3236c 3612851 p.His89Leu missense_variant 0.2
fbiA 3640990 p.Cys150Arg missense_variant 0.13
fbiB 3641388 c.-147C>A upstream_gene_variant 0.15
fbiB 3641900 c.366G>T synonymous_variant 0.14
alr 3841041 p.Asp127Val missense_variant 0.2
ddn 3986797 c.-47A>T upstream_gene_variant 0.15
clpC1 4038428 c.2277G>C synonymous_variant 0.13
clpC1 4038752 p.Gln651His missense_variant 0.12
clpC1 4039132 p.Val525Ile missense_variant 0.18
clpC1 4040069 c.636G>T synonymous_variant 0.17
clpC1 4040457 c.247delC frameshift_variant 0.17
clpC1 4040792 c.-89delG upstream_gene_variant 0.33
embC 4240177 p.Leu105Phe missense_variant 0.14
embC 4240195 p.Lys111Asn missense_variant 0.17
embC 4241872 c.2010G>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243845 p.Ala205Ser missense_variant 0.15
embB 4247840 p.Gly443Cys missense_variant 0.12
embB 4247848 p.Gln445His missense_variant 0.11
embB 4248131 p.Arg540Ser missense_variant 0.12
embB 4248422 p.Ala637Thr missense_variant 0.17
embB 4248781 p.Glu756Asp missense_variant 0.2
embB 4248993 p.Asn827Ile missense_variant 0.17
embB 4249732 c.3219C>A synonymous_variant 0.18
aftB 4267589 c.1248G>A synonymous_variant 0.18
aftB 4268170 p.Ala223Ser missense_variant 0.12
aftB 4268776 c.60delG frameshift_variant 0.22
ethA 4327893 c.-420C>T upstream_gene_variant 0.14
whiB6 4338471 p.Arg17Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338701 c.-180T>C upstream_gene_variant 1.0
gid 4408337 c.-135C>A upstream_gene_variant 0.17