TB-Profiler result

Run: SRR6896534
Summary

Run ID: SRR6896534

Sample name:

Date: 04-04-2023 18:09:05

Number of reads: 139200

Percentage reads mapped: 14.12

Strain:

Drug-resistance: Sensitive

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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
lineage4.4.1.1 Euro-American S;Orphans 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7526 c.225G>C synonymous_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 p.Pro108Gln missense_variant 0.2
gyrA 9037 p.Ala579Asp missense_variant 0.13
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620723 p.Tyr278Ser missense_variant 0.2
rpoB 760171 p.Thr122Arg missense_variant 0.13
rpoB 760720 p.Val305Asp missense_variant 0.2
rpoB 761522 c.1716C>T synonymous_variant 0.2
rpoB 762654 p.Ala950Thr missense_variant 0.67
rpoC 764196 p.Ser276Leu missense_variant 0.25
rpoC 764405 p.Arg346Gly missense_variant 0.25
rpoC 764965 p.Phe532Leu missense_variant 0.12
rpoC 765049 c.1680G>A synonymous_variant 0.13
rpoC 767084 p.Asn1239Tyr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777041 c.1440G>A synonymous_variant 0.15
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpL5 777922 p.Thr187Ser missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800861 p.Asp18Gly missense_variant 0.17
fbiC 1302961 p.Ala11Thr missense_variant 0.18
fbiC 1304906 p.Ala659Val missense_variant 0.33
embR 1416862 c.486T>C synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.18
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.18
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.18
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.22
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.25
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.25
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.25
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.2
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.17
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.17
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.17
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.17
rrl 1474180 n.523T>A non_coding_transcript_exon_variant 0.18
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.18
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.18
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.18
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.38
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.38
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.38
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.36
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.36
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.31
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
rrl 1476447 n.2790T>C non_coding_transcript_exon_variant 0.2
rpsA 1833994 c.453G>T synonymous_variant 0.15
rpsA 1834964 c.1428delA frameshift_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155395 c.717G>C synonymous_variant 1.0
katG 2155406 p.Asn236Asp missense_variant 1.0
katG 2155407 c.705G>C synonymous_variant 1.0
katG 2155410 c.702G>C synonymous_variant 1.0
katG 2155413 c.699G>A synonymous_variant 1.0
katG 2155434 c.678G>C synonymous_variant 1.0
katG 2155446 c.666G>C synonymous_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169610 p.Gly335Ser missense_variant 0.22
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2221813 p.Leu451* stop_gained 0.22
Rv1979c 2222139 c.1026C>T synonymous_variant 0.13
Rv1979c 2223218 c.-54C>T upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714537 p.Ser266Gly missense_variant 0.18
pepQ 2859418 p.Gly334Val missense_variant 0.22
Rv2752c 3065242 p.Arg317Pro missense_variant 1.0
thyX 3067528 p.Arg140Cys missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087527 c.712delG frameshift_variant 0.12
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612356 c.760dupG frameshift_variant 0.4
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3641946 p.Glu138Gln missense_variant 0.67
clpC1 4039470 p.Ile412Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245894 p.Tyr888His missense_variant 0.33
embB 4246490 c.-24G>A upstream_gene_variant 0.22
embB 4247999 p.Asp496Asn missense_variant 0.2
ubiA 4269402 p.His144Gln missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0