TB-Profiler result

Run: SRR7517755

Summary

Run ID: SRR7517755

Sample name:

Date: 04-04-2023 19:35:59

Number of reads: 776242

Percentage reads mapped: 96.01

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.99
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
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
ethA 4326480 p.Glu332* stop_gained 0.43 ethionamide
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6277 c.1038C>A synonymous_variant 0.22
gyrB 6770 p.Thr511Ala missense_variant 0.13
gyrA 7290 c.-12A>G upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491172 c.390C>A synonymous_variant 0.18
fgd1 491310 c.528C>A synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
ccsA 619729 c.-162G>T upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763055 p.Leu1083Phe missense_variant 0.25
rpoC 763531 c.162G>C synonymous_variant 0.92
rpoC 763602 p.Cys78Tyr missense_variant 0.22
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764809 c.1440C>T synonymous_variant 1.0
rpoC 765193 p.Glu608Asp missense_variant 0.19
rpoC 765558 p.Thr730Met missense_variant 0.18
rpoC 765986 p.Leu873Met missense_variant 0.21
rpoC 766544 p.Glu1059* stop_gained 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776094 p.Arg796His missense_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776383 p.Asp700Tyr missense_variant 0.33
mmpL5 776386 p.Pro699Thr missense_variant 0.22
mmpL5 776650 p.Asp611Tyr missense_variant 0.4
mmpL5 776945 p.Glu512Asp missense_variant 0.2
mmpL5 778419 p.Arg21Leu missense_variant 0.23
mmpS5 778784 p.Pro41Gln missense_variant 0.22
mmpL5 778867 c.-387C>A upstream_gene_variant 0.33
mmpL5 779133 c.-653G>T upstream_gene_variant 0.22
mmpS5 779609 c.-704C>A upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302821 c.-110G>A upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406753 c.588C>A synonymous_variant 0.18
Rv1258c 1407078 p.Gly88Val missense_variant 0.2
Rv1258c 1407350 c.-10C>A upstream_gene_variant 0.2
embR 1416228 p.His374Asn missense_variant 0.21
embR 1416802 c.546C>A synonymous_variant 0.33
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417141 c.207C>A synonymous_variant 0.27
embR 1417314 p.Asp12Tyr missense_variant 0.25
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472246 n.401G>T non_coding_transcript_exon_variant 0.4
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.5
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.5
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.5
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.5
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.5
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.5
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.5
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.33
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.33
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.33
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.29
rrl 1473747 n.90C>A non_coding_transcript_exon_variant 0.67
rrl 1475071 n.1414G>T non_coding_transcript_exon_variant 0.67
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.5
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.4
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.5
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.67
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.5
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.5
inhA 1673772 c.-430C>A upstream_gene_variant 0.2
fabG1 1673790 p.Phe117Leu missense_variant 0.25
fabG1 1673840 p.Arg134Leu missense_variant 0.25
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674320 p.Gly40Val missense_variant 0.18
rpsA 1834128 p.Ser196Tyr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102292 p.Asp251Asn missense_variant 0.2
ndh 2103170 c.-128G>A upstream_gene_variant 0.22
katG 2154187 p.Pro642Gln missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155053 c.1059C>T synonymous_variant 0.29
katG 2155100 p.Gly338Cys missense_variant 0.25
katG 2156261 c.-150C>A upstream_gene_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Glu missense_variant 0.4
PPE35 2167969 p.Pro882Thr missense_variant 0.4
PPE35 2168041 p.Ala858Ser missense_variant 0.25
PPE35 2169743 c.870G>T synonymous_variant 0.33
PPE35 2169961 p.Gly218Cys missense_variant 0.33
PPE35 2170115 c.498G>T synonymous_variant 0.2
PPE35 2170493 c.120G>T synonymous_variant 0.29
PPE35 2170602 p.Ser4* stop_gained 0.29
PPE35 2170614 c.-2C>A upstream_gene_variant 0.33
Rv1979c 2221893 c.1272C>A synonymous_variant 0.25
Rv1979c 2222105 p.Ala354Ser missense_variant 0.25
Rv1979c 2222205 c.960G>A synonymous_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222448 c.717G>T synonymous_variant 0.25
Rv1979c 2222454 c.711G>T synonymous_variant 0.22
Rv1979c 2222623 p.Gly181Val missense_variant 0.2
Rv1979c 2222821 p.Ser115* stop_gained 0.33
Rv1979c 2222947 p.Arg73Ile missense_variant 0.2
Rv1979c 2223034 p.Gly44Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289888 c.-647G>T upstream_gene_variant 0.33
pncA 2289901 c.-660G>T upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2715093 c.240C>A synonymous_variant 0.2
eis 2715404 c.-72G>T upstream_gene_variant 0.25
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726518 p.Pro109Gln missense_variant 0.3
ahpC 2726594 c.402G>T synonymous_variant 0.33
folC 2747223 p.Glu126* stop_gained 0.24
pepQ 2859402 p.Glu339Asp missense_variant 0.2
pepQ 2860463 c.-45C>A upstream_gene_variant 0.25
ribD 2987045 p.Phe69Leu missense_variant 0.31
thyA 3073920 c.552C>A synonymous_variant 0.2
ald 3086768 c.-52G>T upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448875 c.372G>T synonymous_variant 0.23
Rv3083 3449317 p.Glu272* stop_gained 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474048 c.42G>T synonymous_variant 0.2
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475309 p.Glu435* stop_gained 0.33
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612103 p.Leu338Phe missense_variant 0.22
Rv3236c 3612240 p.Val293Ile missense_variant 0.18
Rv3236c 3612814 c.303C>A synonymous_variant 0.17
fbiA 3640502 c.-41C>A upstream_gene_variant 0.4
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640705 p.Gly55Trp missense_variant 0.19
fbiB 3642760 p.Arg409Leu missense_variant 0.21
fbiB 3642857 c.1323C>A synonymous_variant 0.25
rpoA 3877882 p.Ala209Glu missense_variant 0.22
rpoA 3878377 p.Ser44* stop_gained 0.31
rpoA 3878386 p.Thr41Asn missense_variant 0.15
ddn 3986815 c.-29G>T upstream_gene_variant 0.22
clpC1 4038503 p.Met734Ile missense_variant 0.22
clpC1 4038691 p.Asp672Tyr missense_variant 0.33
clpC1 4038911 c.1794G>A synonymous_variant 0.5
clpC1 4038938 p.Phe589Leu missense_variant 0.4
clpC1 4038947 c.1758C>T synonymous_variant 0.33
clpC1 4039993 p.Val238Met missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4043993 c.289C>A synonymous_variant 0.24
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242169 c.2307G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243437 p.Ala69Ser missense_variant 0.2
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244329 p.Ala366Val missense_variant 0.25
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248675 p.Ser721Tyr missense_variant 0.25
embB 4249029 p.Pro839His missense_variant 0.21
embB 4249065 p.Gly851Val missense_variant 1.0
aftB 4267091 c.1746C>A synonymous_variant 0.25
aftB 4267621 p.Gly406Cys missense_variant 0.2
aftB 4267980 p.Arg286Leu missense_variant 0.22
aftB 4268618 c.219G>T synonymous_variant 0.67
aftB 4268693 c.144C>A synonymous_variant 0.21
aftB 4269144 c.-308C>A upstream_gene_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4327025 p.Arg150Ile missense_variant 0.2
ethA 4327276 p.Phe66Leu missense_variant 0.2
ethR 4327570 p.Gln8Lys missense_variant 0.23
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407935 p.Leu90Phe missense_variant 1.0