TB-Profiler result

Run: SRR11972258
Summary

Run ID: SRR11972258

Sample name:

Date: 03-04-2023 05:33:51

Number of reads: 371960

Percentage reads mapped: 98.56

Strain: lineage1.1.3

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
lineage1 Indo-Oceanic EAI RD239 0.95
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.92
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.96
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
inhA 1674485 p.Ile95Thr missense_variant 0.5 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 5638 c.399C>T synonymous_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6436 c.-866C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7426 c.127delG frameshift_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.96
gyrA 8798 c.1497C>T synonymous_variant 0.15
gyrA 8986 p.Ser562Tyr missense_variant 0.18
gyrA 9143 c.1842T>C synonymous_variant 0.73
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.38
ccsA 620772 p.Trp294* stop_gained 0.29
rpoB 760223 c.417T>A synonymous_variant 0.2
rpoB 760229 c.423C>T synonymous_variant 0.17
rpoB 761344 p.Val513Glu missense_variant 0.18
rpoB 762063 p.Ala753Thr missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763561 c.192G>A synonymous_variant 0.29
rpoC 763603 c.234C>T synonymous_variant 0.29
rpoC 763884 p.Ala172Val missense_variant 0.91
rpoC 763886 c.517C>A synonymous_variant 0.86
rpoC 765171 p.Pro601Leu missense_variant 0.9
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766069 c.2700G>A synonymous_variant 0.25
rpoC 766367 p.Ala1000Thr missense_variant 0.17
rpoC 767320 c.3951G>T stop_lost&splice_region_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775759 p.Thr908Ala missense_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.78
mmpL5 777590 c.891G>A synonymous_variant 0.17
mmpL5 778021 p.Ala154Pro missense_variant 0.22
mmpL5 778086 c.394delG frameshift_variant 0.18
mmpR5 778283 c.-707G>T upstream_gene_variant 0.2
mmpL5 778471 p.Gln4* stop_gained 0.25
mmpS5 779512 c.-607C>T upstream_gene_variant 0.13
mmpS5 779645 c.-740C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800634 c.-175T>C upstream_gene_variant 0.12
rplC 800836 p.Lys10Glu missense_variant 0.12
rplC 800902 p.Gly32Arg missense_variant 0.13
rplC 801327 p.Asp173Glu missense_variant 0.14
rplC 801390 c.584delA frameshift_variant 0.15
Rv1258c 1407435 c.-95G>A upstream_gene_variant 0.29
embR 1416666 p.Tyr228His missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673367 c.-72delA upstream_gene_variant 0.13
rpsA 1833468 c.-74T>A upstream_gene_variant 0.17
rpsA 1834112 p.Leu191Met missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.3
rpsA 1834959 p.Leu473Gln missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918265 p.Val109Ala missense_variant 0.22
ndh 2101989 p.Ala352Thr missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155988 p.Arg42Trp missense_variant 0.22
katG 2156114 c.-3G>T upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.71
PPE35 2169029 p.Asp528Asn missense_variant 0.29
PPE35 2169041 c.1572G>A synonymous_variant 0.5
PPE35 2169044 c.1569G>C synonymous_variant 0.3
PPE35 2169047 p.Ile522Val missense_variant 0.3
PPE35 2169053 c.1560T>C synonymous_variant 0.8
PPE35 2169056 c.1557A>G synonymous_variant 0.3
PPE35 2169059 c.1554G>A synonymous_variant 0.5
PPE35 2169063 p.Met517Thr missense_variant 0.8
PPE35 2169065 p.Ala516Ile missense_variant 0.5
PPE35 2169068 c.1545G>T synonymous_variant 0.5
PPE35 2169071 c.1542A>G synonymous_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289183 p.Ala20Val missense_variant 0.2
pncA 2290099 c.-858C>T upstream_gene_variant 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714808 p.Phe175Leu missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88
folC 2746438 c.1161G>A synonymous_variant 0.22
folC 2746874 p.Met242Thr missense_variant 0.22
folC 2747544 p.Pro19Ser missense_variant 0.4
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065735 p.Ala153Thr missense_variant 0.4
Rv2752c 3065783 p.Gly137Ser missense_variant 0.29
thyX 3067222 p.Ala242Thr missense_variant 0.17
thyX 3068144 c.-199T>A upstream_gene_variant 0.18
thyA 3074395 p.Thr26Ile missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087085 p.Gln89Arg missense_variant 0.15
ald 3087572 c.753G>A synonymous_variant 0.18
Rv3083 3448514 c.14delT frameshift_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449496 c.993C>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474014 p.Pro3Leu missense_variant 0.57
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3641719 p.Pro62Leu missense_variant 0.2
fbiB 3642156 p.Lys208Glu missense_variant 0.25
fbiB 3642700 p.Ala389Val missense_variant 0.25
alr 3840689 c.732C>T synonymous_variant 1.0
alr 3841253 c.168C>T synonymous_variant 0.94
alr 3841277 c.144C>T synonymous_variant 0.94
rpoA 3878027 c.480delG frameshift_variant 0.15
clpC1 4038397 p.Ala770Ser missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.91
embC 4240671 p.Thr270Ile missense_variant 0.75
embC 4241042 p.Asn394Asp missense_variant 0.8
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.92
embA 4244360 c.1128C>T synonymous_variant 0.15
embA 4244875 p.Pro548Arg missense_variant 0.22
embA 4245969 p.Pro913Ser missense_variant 0.91
embB 4247223 p.Trp237* stop_gained 0.2
embB 4247646 p.Glu378Ala missense_variant 0.67
aftB 4267768 c.1069C>T synonymous_variant 0.14
ubiA 4268959 p.Ile292Lys missense_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.7
ethR 4327362 c.-187G>T upstream_gene_variant 0.14
ethR 4327820 p.Ala91Val missense_variant 0.18
ethA 4328148 c.-675C>T upstream_gene_variant 0.29
ethA 4328222 c.-749G>A upstream_gene_variant 0.22
ethA 4328251 c.-778G>A upstream_gene_variant 0.18
ethA 4328287 c.-814G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0