TB-Profiler result

Run: ERR216978
Summary

Run ID: ERR216978

Sample name:

Date: 31-03-2023 15:57:33

Number of reads: 1208582

Percentage reads mapped: 97.19

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.97
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.97
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
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 6140 p.Val301Leu missense_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491186 p.Ser135Leu missense_variant 0.14
mshA 575739 p.Ala131Val missense_variant 0.29
ccsA 620843 p.His318Arg missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765218 p.Glu617* stop_gained 0.12
rpoC 765472 c.2103C>A synonymous_variant 0.14
rpoC 766961 p.Gly1198Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777594 p.Glu296Ala missense_variant 0.13
mmpL5 777599 p.Asp294Glu missense_variant 0.12
mmpR5 778160 c.-830C>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781485 c.-75C>T upstream_gene_variant 0.12
fbiC 1303701 c.771C>G synonymous_variant 0.14
Rv1258c 1406898 p.Ala148Glu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472486 n.641A>G non_coding_transcript_exon_variant 0.2
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.18
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.36
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.31
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.24
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.28
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.25
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.13
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.12
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.15
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.14
rrl 1473833 n.176_177insT non_coding_transcript_exon_variant 0.15
rrl 1473844 n.187C>T non_coding_transcript_exon_variant 0.13
rrl 1474135 n.478G>A non_coding_transcript_exon_variant 0.43
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.43
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.3
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.29
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.27
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.27
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.27
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.29
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.19
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.33
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.33
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.33
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.29
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.45
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 0.25
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.2
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.2
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 0.22
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.25
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.25
rrl 1475481 n.1824C>G non_coding_transcript_exon_variant 0.25
rrl 1475482 n.1825A>G non_coding_transcript_exon_variant 0.2
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.17
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.15
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.11
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.12
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.12
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.19
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.15
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.15
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.14
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.17
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.27
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.27
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.27
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.27
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.27
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.27
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.29
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.28
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.28
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.28
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.25
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.5
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.5
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.25
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.25
inhA 1674194 c.-8G>A upstream_gene_variant 0.11
inhA 1674406 p.Glu69Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154675 c.1437G>T synonymous_variant 0.13
katG 2155690 p.Leu141Ser missense_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714568 c.765C>A synonymous_variant 0.12
pepQ 2859487 p.Thr311Lys missense_variant 0.12
pepQ 2860569 c.-151G>T upstream_gene_variant 0.12
thyX 3067495 p.Glu151Lys missense_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339054 c.-64C>T upstream_gene_variant 0.18
Rv3083 3448882 p.Glu127Lys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474168 c.162G>A synonymous_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878569 c.-62C>G upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.15
clpC1 4040220 p.Ser162Tyr missense_variant 0.15
embC 4240128 c.272_286delCCGCCGGACTGGCCG disruptive_inframe_deletion 0.2
embC 4240145 p.Ala95Ser missense_variant 0.2
embC 4240441 p.Phe193Leu missense_variant 0.14
embC 4240509 p.Ala216Val missense_variant 0.18
embC 4241539 c.1677T>C synonymous_variant 0.93
embC 4242425 p.Arg855Gly missense_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243394 c.162C>T synonymous_variant 0.12
embA 4244713 p.Ala494Asp missense_variant 0.13
embB 4245566 c.-948C>T upstream_gene_variant 0.14
embA 4245645 p.Ala805Thr missense_variant 0.12
embB 4245785 c.-729G>A upstream_gene_variant 0.22
embB 4249624 c.3111C>G synonymous_variant 0.1
ubiA 4268939 p.Val299Ile missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.96