TB-Profiler result

Run: SRR11972257
Summary

Run ID: SRR11972257

Sample name:

Date: 03-04-2023 05:33:48

Number of reads: 321625

Percentage reads mapped: 99.33

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 0.12
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.95
lineage1.1.3.1 Indo-Oceanic NA RD239 0.87
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 2289190 p.Ser18Pro missense_variant 0.18 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 5969 p.His244Asn missense_variant 0.17
gyrB 6112 p.Met291Ile missense_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8122 p.Leu274Ser missense_variant 0.22
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620221 p.Tyr111His missense_variant 0.12
ccsA 620348 p.Gly153Glu missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763454 p.Lys29Glu missense_variant 0.15
rpoC 763504 c.135C>T synonymous_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 765352 c.1983G>T synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.5
mmpL5 776816 c.1665T>C synonymous_variant 0.12
mmpL5 777259 p.Leu408Met missense_variant 0.2
mmpL5 777433 p.Ala350Thr missense_variant 0.14
mmpL5 777572 c.909C>T synonymous_variant 0.79
mmpR5 778135 c.-855G>A upstream_gene_variant 0.18
mmpL5 778280 p.Asp67Glu missense_variant 0.12
mmpS5 779613 c.-708C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303600 p.Glu224Lys missense_variant 0.13
fbiC 1304716 p.Ala596Thr missense_variant 0.14
fbiC 1304720 p.Thr597Ile missense_variant 0.14
fbiC 1304933 p.Ala668Val missense_variant 0.15
Rv1258c 1406823 p.Thr173Ile missense_variant 0.15
embR 1416237 p.Ile371Val missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472196 n.351C>T non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1304delG non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21
rrl 1474160 n.503C>T non_coding_transcript_exon_variant 0.18
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.12
inhA 1674272 p.His24Arg missense_variant 0.13
inhA 1674355 p.Asp52Asn missense_variant 0.22
rpsA 1833370 c.-172G>C upstream_gene_variant 1.0
rpsA 1833740 p.Glu67Lys missense_variant 0.15
rpsA 1834282 c.741C>T synonymous_variant 0.12
rpsA 1834313 p.Val258Ile missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918315 p.Pro126Thr missense_variant 0.33
tlyA 1918580 p.Arg214Leu missense_variant 0.25
ndh 2102254 c.789C>T synonymous_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154961 p.Leu384Pro missense_variant 0.25
katG 2155827 c.285C>T synonymous_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.17
PPE35 2167874 c.2739C>T synonymous_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.77
PPE35 2167983 p.Gly877Asp missense_variant 0.73
PPE35 2169436 p.Asn393Asp missense_variant 0.18
Rv1979c 2222227 p.Phe313Ser missense_variant 0.22
Rv1979c 2222246 p.Gly307Arg missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289433 c.-192C>T upstream_gene_variant 0.22
pncA 2289903 c.-662C>A upstream_gene_variant 0.15
pncA 2289954 c.-713A>G upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.9
ahpC 2726373 p.Cys61Arg missense_variant 0.14
pepQ 2859446 p.Glu325Gln missense_variant 0.25
pepQ 2859566 p.Gly285Ser missense_variant 0.14
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065975 p.Asp73Asn missense_variant 0.18
Rv2752c 3067096 c.-905C>T upstream_gene_variant 0.22
thyX 3067367 c.579G>A synonymous_variant 0.22
thyA 3074189 p.Gly95Cys missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.81
ald 3087009 p.Val64Leu missense_variant 0.14
fbiD 3339431 p.Glu105Gly missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449167 p.Ala222Thr missense_variant 0.5
Rv3083 3449839 p.Arg446Gly missense_variant 0.33
Rv3083 3449846 p.Gln448Arg missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.89
fprA 3474297 p.Tyr97* stop_gained 0.2
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612725 p.Gly131Asp missense_variant 0.2
fbiA 3640973 p.Pro144Leu missense_variant 0.25
fbiA 3641120 p.Ser193Phe missense_variant 0.33
fbiB 3642434 c.900G>A synonymous_variant 0.2
alr 3841181 c.240C>A synonymous_variant 0.12
alr 3841253 c.168C>T synonymous_variant 0.94
alr 3841277 c.144C>T synonymous_variant 0.95
rpoA 3877709 p.Glu267* stop_gained 0.13
rpoA 3877789 p.Glu240Val missense_variant 0.12
clpC1 4039498 p.Ile403Val missense_variant 0.22
clpC1 4039691 c.1014G>C synonymous_variant 0.17
clpC1 4039729 p.Asp326Asn missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 0.9
embC 4240671 p.Thr270Ile missense_variant 0.93
embC 4240768 c.906G>T synonymous_variant 0.22
embC 4241042 p.Asn394Asp missense_variant 0.68
embC 4241889 p.Ala676Val missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243370 c.138G>A synonymous_variant 0.18
embA 4243792 p.Ala187Val missense_variant 0.13
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245013 p.Arg594His missense_variant 0.25
embB 4245899 c.-615C>T upstream_gene_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 0.83
embB 4246752 p.Thr80Ile missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249658 p.Met1049Val missense_variant 0.11
aftB 4267080 p.Arg586Gln missense_variant 0.15
aftB 4267309 p.Leu510Met missense_variant 0.2
aftB 4268711 p.Leu42Phe missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 0.91
aftB 4269606 c.-770T>C upstream_gene_variant 0.62
ethA 4327179 p.Arg99Trp missense_variant 0.15
ethA 4328337 c.-864C>T upstream_gene_variant 0.25
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407740 p.Pro155Ser missense_variant 0.15
gid 4407780 c.423G>A synonymous_variant 0.91
gid 4407835 p.Trp123* stop_gained 0.15
gid 4407873 c.330G>T synonymous_variant 0.91
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0