TB-Profiler result

Run: SRR6789628
Summary

Run ID: SRR6789628

Sample name:

Date: 04-04-2023 16:04:16

Number of reads: 897996

Percentage reads mapped: 93.57

Strain: lineage4.9

Drug-resistance: HR-TB

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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
katG 2155740 c.371delG frameshift_variant 0.14 isoniazid, isoniazid
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 6652 c.-650C>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576092 p.Pro249Ser missense_variant 0.12
ccsA 619864 c.-27G>A upstream_gene_variant 0.11
rpoB 760960 p.Val385Ala missense_variant 0.1
rpoB 760965 p.Met387Leu missense_variant 0.1
rpoB 760970 c.1164G>C synonymous_variant 0.1
rpoB 760982 c.1176G>C synonymous_variant 0.1
rpoB 760985 c.1179G>C synonymous_variant 0.11
rpoB 760988 c.1182C>G synonymous_variant 0.1
rpoB 760991 c.1185G>C synonymous_variant 0.1
rpoB 760997 c.1191G>C synonymous_variant 0.11
rpoB 761554 p.Val583Ala missense_variant 0.1
rpoB 761564 c.1758G>C synonymous_variant 0.11
rpoB 761565 p.Met587Leu missense_variant 0.1
rpoB 761573 c.1767C>G synonymous_variant 0.12
rpoB 761579 c.1773G>C synonymous_variant 0.11
rpoB 761600 c.1794T>C synonymous_variant 0.11
rpoB 761603 c.1797C>G synonymous_variant 0.11
rpoC 764302 c.933C>A synonymous_variant 0.12
rpoC 764344 c.975C>A synonymous_variant 0.11
rpoC 764361 p.Asp331Gly missense_variant 0.1
rpoC 764441 p.Ile358Leu missense_variant 0.11
rpoC 764446 c.1077T>C synonymous_variant 0.1
rpoC 764449 c.1080G>C synonymous_variant 0.1
rpoC 764452 c.1083T>C synonymous_variant 0.1
rpoC 764461 c.1092A>G synonymous_variant 0.11
rpoC 764485 c.1116G>C synonymous_variant 0.17
rpoC 764491 c.1122G>C synonymous_variant 0.17
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764498 p.Ser377Ala missense_variant 0.15
rpoC 764507 p.Ala380Ser missense_variant 0.15
rpoC 764521 c.1152T>C synonymous_variant 0.12
rpoC 764539 c.1170C>G synonymous_variant 0.1
rpoC 764560 c.1191T>C synonymous_variant 0.12
rpoC 765558 p.Thr730Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778092 c.388delT frameshift_variant 0.11
mmpS5 778710 p.Tyr66His missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303891 p.Ala321Ser missense_variant 0.11
fbiC 1305068 p.Val713Ala missense_variant 0.14
atpE 1461000 c.-45C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.15
rrs 1473022 n.1177G>A non_coding_transcript_exon_variant 0.16
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.16
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.16
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.22
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.26
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.24
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.19
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.19
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.17
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.11
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.15
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.15
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.13
rrl 1474711 n.1054_1055insAA non_coding_transcript_exon_variant 0.12
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.1
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.12
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.12
rrl 1474784 n.1127C>T non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
rpsA 1833856 c.315A>G synonymous_variant 0.1
rpsA 1833862 c.321G>C synonymous_variant 0.1
rpsA 1833874 c.333T>C synonymous_variant 0.12
rpsA 1833886 c.345C>G synonymous_variant 0.11
rpsA 1833893 p.Ala118Pro missense_variant 0.11
rpsA 1833970 c.429G>C synonymous_variant 0.13
rpsA 1833979 c.438T>C synonymous_variant 0.14
rpsA 1833985 c.444G>C synonymous_variant 0.15
rpsA 1833988 c.447C>G synonymous_variant 0.15
rpsA 1833994 c.453G>C synonymous_variant 0.14
rpsA 1833997 c.456G>C synonymous_variant 0.11
rpsA 1834012 c.471G>C synonymous_variant 0.12
rpsA 1834025 p.Gln162Ala missense_variant 0.11
rpsA 1834040 p.Lys167Gln missense_variant 0.11
rpsA 1834043 p.Glu168Lys missense_variant 0.11
rpsA 1834046 p.Ile169Leu missense_variant 0.13
rpsA 1834054 c.513C>G synonymous_variant 0.13
rpsA 1834093 c.552G>C synonymous_variant 0.16
rpsA 1834102 c.561T>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102225 p.Cys273Tyr missense_variant 0.11
katG 2154852 p.Met420Ile missense_variant 0.11
katG 2155836 c.276C>A synonymous_variant 0.13
PPE35 2169402 p.Thr404Met missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.51
Rv1979c 2222074 p.Pro364Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518028 c.-87G>T upstream_gene_variant 0.11
eis 2715483 c.-151C>A upstream_gene_variant 0.18
folC 2746823 p.Glu259Val missense_variant 0.13
pepQ 2859871 p.His183Leu missense_variant 0.33
pepQ 2860165 p.Gly85Asp missense_variant 0.15
ribD 2987551 p.Met238Lys missense_variant 0.25
thyX 3067273 c.672delC frameshift_variant 0.17
fbiD 3339469 p.Pro118Thr missense_variant 0.17
Rv3083 3448334 c.-170C>A upstream_gene_variant 0.11
Rv3083 3449417 p.Leu305Gln missense_variant 0.17
Rv3236c 3611964 p.Asn385Tyr missense_variant 0.14
clpC1 4039430 c.1275T>C synonymous_variant 0.11
clpC1 4039454 c.1251A>T synonymous_variant 0.12
clpC1 4039463 c.1242C>G synonymous_variant 0.12
clpC1 4039466 c.1239T>C synonymous_variant 0.12
clpC1 4039469 c.1236T>C synonymous_variant 0.12
clpC1 4039472 c.1233G>C synonymous_variant 0.12
clpC1 4039478 c.1227G>C synonymous_variant 0.12
clpC1 4039481 c.1224T>C synonymous_variant 0.14
clpC1 4039487 c.1218G>C synonymous_variant 0.15
clpC1 4039522 c.1183C>T synonymous_variant 0.17
clpC1 4039528 c.1177C>A synonymous_variant 0.18
clpC1 4039559 c.1146C>G synonymous_variant 0.14
clpC1 4039562 c.1143C>G synonymous_variant 0.14
clpC1 4039570 p.Met379Leu missense_variant 0.16
clpC1 4040164 p.Ala181Ser missense_variant 0.14
embA 4244124 p.Gly298Cys missense_variant 0.11
embA 4244875 p.Pro548Gln missense_variant 0.15
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.28
embB 4246586 p.Gly25Trp missense_variant 0.12
embB 4249190 c.2682delC frameshift_variant 0.12
embB 4249501 p.Cys996* stop_gained 0.11
embB 4249734 p.Pro1074His missense_variant 0.13
aftB 4268611 p.Pro76Thr missense_variant 0.33
ubiA 4269013 p.Pro274Leu missense_variant 0.12
ubiA 4269249 p.Glu195Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407916 p.Arg96His missense_variant 1.0