TB-Profiler result

Run: SRR4035722
Summary

Run ID: SRR4035722

Sample name:

Date: 04-04-2023 07:15:30

Number of reads: 1296558

Percentage reads mapped: 99.39

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 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
embB 4246734 p.Leu74Arg missense_variant 0.11 ethambutol
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 5130 c.-110A>G upstream_gene_variant 0.13
gyrB 5308 c.69G>A synonymous_variant 0.13
gyrB 7112 p.Thr625Ala missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7590 p.Val97Met missense_variant 0.12
gyrA 7921 p.Asn207Ile missense_variant 0.14
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8399 c.1098T>C synonymous_variant 0.12
gyrA 9036 p.Ala579Thr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9313 p.Leu671Arg missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575420 p.Thr25Ala missense_variant 0.1
mshA 575651 p.Arg102Trp missense_variant 0.14
mshA 576593 p.Val416Met missense_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760767 p.Pro321Ser missense_variant 0.2
rpoB 761136 p.Thr444Ala missense_variant 0.18
rpoB 761192 c.1389delG frameshift_variant 0.2
rpoB 762082 p.Gly759Ala missense_variant 0.17
rpoB 762306 p.Pro834Ser missense_variant 0.22
rpoC 763094 c.-276G>T upstream_gene_variant 0.14
rpoC 763115 c.-255T>C upstream_gene_variant 0.14
rpoC 764210 p.Ile281Val missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764399 p.Tyr344His missense_variant 0.1
rpoC 765137 p.Thr590Ser missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765438 c.2070delG frameshift_variant 0.14
rpoC 766073 p.Ala902Pro missense_variant 0.11
rpoC 766076 p.Glu903Gln missense_variant 0.11
rpoC 766862 p.Val1165Leu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776481 p.Ala667Val missense_variant 0.14
mmpL5 776492 p.Gln663His missense_variant 0.2
mmpL5 776714 c.1766delA frameshift_variant 0.14
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777437 c.1044C>T synonymous_variant 0.17
mmpL5 777532 p.Ile317Val missense_variant 0.17
mmpL5 777762 p.Leu240Gln missense_variant 0.17
mmpL5 777986 c.495C>T synonymous_variant 0.18
mmpL5 778188 p.Gln98Arg missense_variant 0.11
mmpL5 778386 p.Ala32Val missense_variant 0.17
mmpS5 779635 c.-730G>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303442 p.Leu171Ser missense_variant 0.13
fbiC 1303794 c.864A>G synonymous_variant 0.13
fbiC 1303818 c.889delG frameshift_variant 0.14
fbiC 1303942 p.Val338Met missense_variant 0.13
fbiC 1304222 c.1295delG frameshift_variant 0.25
fbiC 1304434 p.Ala502Ser missense_variant 0.15
embR 1417112 p.Leu79Pro missense_variant 0.15
atpE 1460855 c.-189delC upstream_gene_variant 0.12
atpE 1461042 c.-3G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471789 n.-57T>C upstream_gene_variant 0.11
rrs 1471796 n.-50A>G upstream_gene_variant 0.12
rrl 1473684 n.27G>A non_coding_transcript_exon_variant 0.12
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.14
rrl 1474058 n.401C>T non_coding_transcript_exon_variant 0.14
rrl 1474296 n.640delC non_coding_transcript_exon_variant 0.22
rrl 1474458 n.801C>A non_coding_transcript_exon_variant 0.17
rrl 1476173 n.2516A>G non_coding_transcript_exon_variant 0.2
rrl 1476306 n.2649A>G non_coding_transcript_exon_variant 0.15
fabG1 1673720 p.Asp94Val missense_variant 0.17
inhA 1674224 p.Lys8Ile missense_variant 0.17
inhA 1674756 c.555T>C synonymous_variant 0.15
rpsA 1833562 c.21C>G synonymous_variant 0.14
rpsA 1834017 p.Arg159His missense_variant 0.22
rpsA 1834218 p.Val226Ala missense_variant 0.18
rpsA 1834361 c.820T>C synonymous_variant 0.18
rpsA 1834752 p.Leu404Pro missense_variant 0.12
tlyA 1917886 c.-54C>A upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918421 p.Ala161Asp missense_variant 0.13
ndh 2101947 p.Asp366Tyr missense_variant 0.14
ndh 2102446 c.597C>T synonymous_variant 0.13
ndh 2102774 p.Thr90Ser missense_variant 0.2
katG 2154049 p.Lys688Thr missense_variant 0.11
katG 2154225 c.1887T>C synonymous_variant 0.17
katG 2154242 p.Met624Leu missense_variant 0.17
katG 2154343 p.Lys590Arg missense_variant 0.12
katG 2154516 c.1596G>T synonymous_variant 0.17
katG 2154540 c.1572C>T synonymous_variant 0.22
katG 2154626 p.Arg496Ser missense_variant 0.25
katG 2154670 p.Ser481Leu missense_variant 0.29
katG 2155723 p.Ala130Gly missense_variant 0.11
katG 2155851 c.261G>A synonymous_variant 0.18
PPE35 2167868 c.2744delG frameshift_variant 0.14
PPE35 2168195 c.2418G>T synonymous_variant 0.12
PPE35 2168541 p.Thr691Ile missense_variant 0.14
PPE35 2168790 p.Pro608Leu missense_variant 0.15
PPE35 2168915 c.1698G>A synonymous_variant 0.25
PPE35 2168964 p.Val550Ala missense_variant 0.14
PPE35 2168991 p.Ala541Asp missense_variant 0.13
PPE35 2169981 p.Asn211Ile missense_variant 0.2
Rv1979c 2222548 p.Ser206* stop_gained 0.2
Rv1979c 2223029 p.Phe46Ile missense_variant 0.14
Rv1979c 2223180 c.-16A>G upstream_gene_variant 0.13
Rv1979c 2223249 c.-85G>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223300 c.-136G>C upstream_gene_variant 0.14
Rv1979c 2223312 c.-148C>A upstream_gene_variant 0.14
Rv1979c 2223316 c.-152T>A upstream_gene_variant 0.14
pncA 2289796 c.-555T>G upstream_gene_variant 0.12
pncA 2290072 c.-831T>C upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518265 p.Val51Leu missense_variant 0.11
kasA 2518290 p.Lys59Thr missense_variant 0.11
eis 2714149 p.Pro395Arg missense_variant 0.11
eis 2714416 p.Glu306Ala missense_variant 0.18
eis 2715128 p.Leu69Met missense_variant 0.17
eis 2715137 p.Asp66Asn missense_variant 0.15
eis 2715147 c.186G>A synonymous_variant 0.14
ahpC 2726450 c.258G>C synonymous_variant 0.11
ahpC 2726579 c.387T>C synonymous_variant 0.11
folC 2746570 c.1029C>T synonymous_variant 0.25
folC 2746816 c.783C>A synonymous_variant 0.17
folC 2747122 c.477G>A synonymous_variant 0.17
folC 2747201 p.Leu133Pro missense_variant 0.15
folC 2747496 p.Asp35Asn missense_variant 0.12
pepQ 2859575 p.Ala282Pro missense_variant 0.2
pepQ 2859580 p.Leu280Pro missense_variant 0.18
pepQ 2860159 p.Ala87Gly missense_variant 0.22
ribD 2986711 c.-128G>A upstream_gene_variant 0.33
ribD 2987158 p.Gln107Arg missense_variant 0.17
Rv2752c 3065376 c.816C>T synonymous_variant 0.17
Rv2752c 3066161 p.Leu11Met missense_variant 0.12
thyX 3067268 c.678G>C synonymous_variant 0.15
thyX 3067282 p.Val222Met missense_variant 0.15
thyX 3067701 p.Ile82Thr missense_variant 0.15
thyX 3067716 p.Ser77Thr missense_variant 0.17
thyA 3073901 p.Gln191Glu missense_variant 0.11
thyA 3074064 c.408C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087788 p.Glu323Asp missense_variant 0.11
fbiD 3338999 c.-119T>G upstream_gene_variant 0.11
fbiD 3339041 c.-77G>A upstream_gene_variant 0.14
fbiD 3339579 c.462C>T synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474226 p.Pro74Ser missense_variant 0.18
fprA 3474764 p.Arg253Leu missense_variant 0.14
whiB7 3568868 c.-189G>T upstream_gene_variant 0.2
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612364 c.753T>C synonymous_variant 0.15
fbiA 3640642 p.His34Asp missense_variant 0.11
fbiA 3641075 p.Ala178Asp missense_variant 0.13
fbiA 3641510 p.Gly323Glu missense_variant 0.17
fbiB 3642209 c.675C>T synonymous_variant 0.14
fbiB 3642635 p.Asp367Glu missense_variant 0.14
fbiB 3642774 p.Leu414Met missense_variant 0.13
alr 3840701 c.719_720insAGAC frameshift_variant 0.14
rpoA 3877533 c.975C>T synonymous_variant 0.14
rpoA 3877907 p.Ser201Pro missense_variant 0.11
rpoA 3878013 c.495T>C synonymous_variant 0.12
clpC1 4040806 c.-102A>T upstream_gene_variant 0.2
panD 4044195 p.Asp29Glu missense_variant 0.17
embC 4240025 p.Thr55Ala missense_variant 0.18
embC 4240814 p.Gly318Ser missense_variant 0.17
embC 4241231 p.Arg457Trp missense_variant 0.13
embC 4241234 p.Thr458Ala missense_variant 0.14
embC 4241279 p.Val473Met missense_variant 0.12
embC 4241844 p.Leu661His missense_variant 0.14
embC 4242219 p.Thr786Arg missense_variant 0.12
embC 4242425 p.Arg855Gly missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242722 p.Pro954Ser missense_variant 0.25
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244510 c.1278G>A synonymous_variant 0.2
embA 4245382 p.Thr717Ile missense_variant 0.14
embB 4246605 p.Thr31Ile missense_variant 0.15
embB 4246625 p.Phe38Leu missense_variant 0.14
embB 4246750 c.237T>C synonymous_variant 0.12
embB 4247986 c.1473C>A synonymous_variant 0.12
embB 4248708 p.Thr732Ser missense_variant 0.12
embB 4249062 p.Thr850Ile missense_variant 0.17
aftB 4267123 c.1714C>A synonymous_variant 0.14
aftB 4267756 p.Lys361Glu missense_variant 0.12
aftB 4268277 p.Pro187Gln missense_variant 0.13
aftB 4268297 c.540A>G synonymous_variant 0.11
aftB 4268384 c.453G>A synonymous_variant 0.15
aftB 4268406 p.Val144Ala missense_variant 0.18
aftB 4268547 p.Leu97Pro missense_variant 0.11
ubiA 4269407 p.Lys143* stop_gained 0.15
ubiA 4269617 p.Asn73Tyr missense_variant 0.17
ubiA 4269634 p.Ser67Leu missense_variant 0.25
ethA 4326345 p.Ile377Val missense_variant 0.29
ethA 4327614 c.-141G>C upstream_gene_variant 0.15
whiB6 4338569 c.-48A>G upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0