TB-Profiler result

Run: SRR13861399
Summary

Run ID: SRR13861399

Sample name:

Date: 03-04-2023 09:30:49

Number of reads: 1373768

Percentage reads mapped: 45.84

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.14 streptomycin
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 6027 p.His263Arg missense_variant 1.0
mshA 576327 p.Phe327Tyr missense_variant 1.0
ccsA 620295 c.405G>C synonymous_variant 0.13
ccsA 620307 c.417C>G synonymous_variant 0.15
rpoB 759707 c.-100C>T upstream_gene_variant 1.0
rpoB 760178 c.372G>C synonymous_variant 0.9
rpoB 760919 c.1113C>G synonymous_variant 0.16
rpoB 760925 c.1119T>C synonymous_variant 0.17
rpoB 760928 c.1122G>C synonymous_variant 0.17
rpoB 760934 c.1128C>T synonymous_variant 0.16
rpoB 760946 c.1140A>G synonymous_variant 0.16
rpoB 760970 c.1164G>C synonymous_variant 0.15
rpoB 760982 c.1176G>C synonymous_variant 0.15
rpoB 760985 c.1179G>C synonymous_variant 0.17
rpoB 760991 c.1185G>C synonymous_variant 0.17
rpoB 761015 c.1209G>C synonymous_variant 0.17
rpoB 761021 c.1215G>C synonymous_variant 0.17
rpoB 761027 c.1221A>G synonymous_variant 0.15
rpoB 761036 c.1230G>C synonymous_variant 0.17
rpoB 761037 c.1231T>C synonymous_variant 0.17
rpoB 762284 c.2478G>A synonymous_variant 1.0
rpoC 764262 p.Val298Ala missense_variant 0.94
rpoC 764389 p.Leu340Phe missense_variant 0.14
rpoC 764431 c.1062G>C synonymous_variant 0.16
rpoC 764434 c.1065A>G synonymous_variant 0.16
rpoC 764446 c.1077T>C synonymous_variant 0.15
rpoC 764449 c.1080G>C synonymous_variant 0.15
rpoC 764455 c.1086G>C synonymous_variant 0.15
rpoC 764458 c.1089G>C synonymous_variant 0.15
rpoC 764461 c.1092A>G synonymous_variant 0.17
rpoC 764497 c.1128A>G synonymous_variant 0.14
rpoC 764530 c.1161C>G synonymous_variant 0.15
rpoC 764536 c.1167G>C synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.14
rpoC 764560 c.1191T>C synonymous_variant 0.15
rpoC 764566 c.1197C>G synonymous_variant 0.14
rpoC 764575 c.1206T>G synonymous_variant 0.13
rpoC 764576 p.Ser403Thr missense_variant 0.13
rpoC 764626 c.1257C>T synonymous_variant 0.13
rpoC 764644 c.1275G>C synonymous_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 765658 c.2289C>T synonymous_variant 0.14
rpoC 765700 c.2331T>C synonymous_variant 0.16
rpoC 765796 c.2427C>T synonymous_variant 0.12
mmpL5 777280 p.Ala401Ser missense_variant 1.0
mmpS5 778853 p.Val18Ala missense_variant 1.0
rpsL 781751 c.192G>C synonymous_variant 0.13
rpsL 781760 c.201T>C synonymous_variant 0.14
rpsL 781793 c.234G>C synonymous_variant 0.15
rpsL 781859 c.300T>C synonymous_variant 0.13
rpsL 781898 c.339A>T synonymous_variant 0.12
rpsL 781916 c.357T>C synonymous_variant 0.15
rpsL 781929 p.Gly124Ser missense_variant 0.15
rplC 800771 c.-38C>T upstream_gene_variant 0.15
rplC 800814 c.6A>G synonymous_variant 0.18
rplC 800817 c.9A>T synonymous_variant 0.18
rplC 800844 c.36T>C synonymous_variant 0.14
rplC 800874 c.66A>G synonymous_variant 0.12
embR 1416662 p.Arg229Pro missense_variant 1.0
rrs 1472028 n.183A>T non_coding_transcript_exon_variant 0.13
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.14
rrs 1472031 n.186G>A non_coding_transcript_exon_variant 0.14
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.13
rrs 1472044 n.199G>C non_coding_transcript_exon_variant 0.14
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.17
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.16
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.14
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.13
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.15
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.15
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.15
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 0.98
rpsA 1834222 c.681T>C synonymous_variant 0.12
rpsA 1834240 c.699T>C synonymous_variant 0.14
rpsA 1834528 c.987T>C synonymous_variant 0.14
rpsA 1834546 c.1005T>C synonymous_variant 0.14
rpsA 1834555 c.1014T>C synonymous_variant 0.14
rpsA 1834558 c.1017C>G synonymous_variant 0.15
rpsA 1834624 c.1083G>C synonymous_variant 0.12
rpsA 1834633 c.1092A>G synonymous_variant 0.14
rpsA 1834666 c.1125G>C synonymous_variant 0.12
rpsA 1834688 c.1147_1148delAGinsTC synonymous_variant 0.12
katG 2155675 p.Arg146Leu missense_variant 0.89
katG 2155701 c.411C>T synonymous_variant 0.14
katG 2155716 c.396T>C synonymous_variant 0.14
Rv1979c 2222433 c.732A>G synonymous_variant 1.0
kasA 2518672 c.558G>C synonymous_variant 0.13
kasA 2518687 c.573C>T synonymous_variant 0.13
kasA 2518702 c.588C>T synonymous_variant 0.12
kasA 2518717 c.603C>T synonymous_variant 0.14
kasA 2518723 p.Glu203Asp missense_variant 0.15
kasA 2518732 c.618C>G synonymous_variant 0.17
kasA 2518741 c.627G>C synonymous_variant 0.17
kasA 2518747 c.633C>G synonymous_variant 0.16
kasA 2518768 c.654C>G synonymous_variant 0.16
kasA 2518783 c.669T>C synonymous_variant 0.16
kasA 2518792 c.678C>G synonymous_variant 0.15
kasA 2518795 c.681C>G synonymous_variant 0.15
thyA 3073872 p.Ile200Val missense_variant 0.14
thyA 3073878 c.594G>A synonymous_variant 0.14
thyA 3073892 c.580T>C synonymous_variant 0.15
thyA 3073893 c.579C>G synonymous_variant 0.15
thyA 3073925 c.547T>C synonymous_variant 0.14
thyA 3073926 c.546G>C synonymous_variant 0.15
thyA 3073929 c.543T>C synonymous_variant 0.15
thyA 3073953 c.519T>C synonymous_variant 0.15
thyA 3074010 c.462C>G synonymous_variant 0.14
ald 3086631 c.-189A>G upstream_gene_variant 1.0
Rv3236c 3612954 c.162delC frameshift_variant 1.0
alr 3840284 p.Trp379* stop_gained 0.97
rpoA 3877743 c.765T>C synonymous_variant 0.14
rpoA 3877776 c.732T>C synonymous_variant 0.13
rpoA 3877782 c.726T>C synonymous_variant 0.14
rpoA 3877818 c.690A>G synonymous_variant 0.16
rpoA 3877839 c.669G>C synonymous_variant 0.17
rpoA 3877857 c.651G>A synonymous_variant 0.19
rpoA 3877866 c.642G>C synonymous_variant 0.17
rpoA 3877872 c.636C>T synonymous_variant 0.17
rpoA 3877875 c.633T>G synonymous_variant 0.19
rpoA 3877899 p.Ser203Thr missense_variant 0.14
rpoA 3877905 c.603A>G synonymous_variant 0.14
rpoA 3877908 p.Asn200Ser missense_variant 0.15
rpoA 3877953 c.555G>A synonymous_variant 0.13
rpoA 3877962 c.546G>T synonymous_variant 0.12
clpC1 4038347 c.2358G>C synonymous_variant 0.14
clpC1 4038536 c.2169C>T synonymous_variant 0.13
clpC1 4038611 c.2094C>T synonymous_variant 0.17
clpC1 4038623 c.2082A>G synonymous_variant 0.15
clpC1 4038653 c.2052C>T synonymous_variant 0.12
clpC1 4038661 p.Ser682Thr missense_variant 0.12
clpC1 4038671 c.2034T>C synonymous_variant 0.13
clpC1 4039073 c.1632C>G synonymous_variant 0.13
clpC1 4039169 p.Glu512Asp missense_variant 0.13
clpC1 4039274 c.1431G>C synonymous_variant 0.13
clpC1 4039388 c.1317C>A synonymous_variant 0.13
clpC1 4039391 c.1314T>G synonymous_variant 0.13
clpC1 4039409 c.1296T>C synonymous_variant 0.14
clpC1 4039412 c.1293T>G synonymous_variant 0.14
clpC1 4039442 c.1263A>G synonymous_variant 0.14
clpC1 4039448 c.1257A>G synonymous_variant 0.16
clpC1 4039454 c.1251A>G synonymous_variant 0.16
clpC1 4039463 c.1242C>G synonymous_variant 0.15
clpC1 4039466 c.1239T>C synonymous_variant 0.14
clpC1 4039469 c.1236T>C synonymous_variant 0.14
embC 4240042 p.Asn60Lys missense_variant 1.0
embC 4240936 c.1074A>G synonymous_variant 0.15
embC 4241050 c.1188T>G synonymous_variant 0.12
embB 4245806 c.-708G>A upstream_gene_variant 0.96
embB 4247075 c.563dupT frameshift_variant 1.0
embB 4247839 c.1326G>A synonymous_variant 0.96
embB 4248070 c.1557T>C synonymous_variant 0.14
embB 4248097 c.1584C>G synonymous_variant 0.13
embB 4248118 c.1605T>C synonymous_variant 0.16
embB 4248127 c.1614G>C synonymous_variant 0.16
embB 4248133 c.1620C>G synonymous_variant 0.16
embB 4248142 c.1629T>C synonymous_variant 0.17
embB 4248143 c.1630T>C synonymous_variant 0.17
embB 4248157 c.1644A>G synonymous_variant 0.19
embB 4248206 p.Ser565Gly missense_variant 0.16
embB 4248220 c.1707A>G synonymous_variant 0.14
embB 4249763 p.Thr1084Pro missense_variant 1.0
ethA 4326860 p.Leu205Pro missense_variant 1.0