TB-Profiler result

Run: SRR9613550
Summary

Run ID: SRR9613550

Sample name:

Date: 04-04-2023 22:54:53

Number of reads: 8542681

Percentage reads mapped: 99.99

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8156 c.855T>C synonymous_variant 0.11
gyrA 8168 c.867A>G synonymous_variant 0.12
gyrA 8324 c.1023T>C synonymous_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.95
rpoB 760115 c.309C>T synonymous_variant 0.98
rpoB 760283 c.477G>C synonymous_variant 0.13
rpoB 760298 c.492G>C synonymous_variant 0.14
rpoB 760316 c.510C>G synonymous_variant 0.11
rpoB 760376 p.Asp190Glu missense_variant 0.12
rpoB 760407 p.Ser201Gly missense_variant 0.13
rpoB 761606 c.1800C>G synonymous_variant 0.14
rpoB 761615 c.1809A>C synonymous_variant 0.13
rpoB 761645 c.1839C>G synonymous_variant 0.11
rpoB 761999 c.2193G>C synonymous_variant 0.13
rpoB 762002 c.2196C>G synonymous_variant 0.12
rpoB 762233 c.2427G>T synonymous_variant 0.14
rpoB 762239 c.2433G>A synonymous_variant 0.18
rpoB 762245 c.2439G>C synonymous_variant 0.18
rpoB 762284 c.2478G>T synonymous_variant 0.16
rpoB 762293 c.2487T>G synonymous_variant 0.15
rpoB 762308 c.2502G>C synonymous_variant 0.12
rpoC 762929 c.-441G>C upstream_gene_variant 0.12
rpoC 762959 c.-411G>C upstream_gene_variant 0.13
rpoC 762962 c.-408C>T upstream_gene_variant 0.14
rpoC 762983 c.-387C>T upstream_gene_variant 0.14
rpoC 762989 c.-381G>A upstream_gene_variant 0.14
rpoC 762995 c.-375G>T upstream_gene_variant 0.15
rpoC 763004 c.-366G>A upstream_gene_variant 0.14
rpoC 763007 c.-363C>T upstream_gene_variant 0.14
rpoC 763022 c.-348C>G upstream_gene_variant 0.12
rpoC 763028 c.-342T>C upstream_gene_variant 0.13
rpoC 763053 c.-317T>C upstream_gene_variant 0.11
rpoC 763546 c.177A>G synonymous_variant 0.11
rpoC 763621 c.252C>T synonymous_variant 0.17
rpoC 763660 c.291T>G synonymous_variant 0.14
rpoC 764320 c.951C>G synonymous_variant 0.1
rpoC 764575 c.1206T>G synonymous_variant 0.15
rpoC 764605 c.1236G>C synonymous_variant 0.16
rpoC 764611 c.1242G>T synonymous_variant 0.15
rpoC 764626 c.1257C>T synonymous_variant 0.18
rpoC 764650 c.1281G>T synonymous_variant 0.16
rpoC 764668 c.1299C>T synonymous_variant 0.17
rpoC 764713 c.1344G>C synonymous_variant 0.16
rpoC 764746 c.1377G>T synonymous_variant 0.19
rpoC 764752 c.1383G>C synonymous_variant 0.17
rpoC 764758 c.1389C>G synonymous_variant 0.16
rpoC 764764 c.1395T>C synonymous_variant 0.17
rpoC 764800 c.1431G>A synonymous_variant 0.14
rpoC 764803 c.1434C>T synonymous_variant 0.14
rpoC 764809 c.1440C>T synonymous_variant 0.14
rpoC 764935 c.1566T>C synonymous_variant 0.13
rpoC 764948 c.1579T>C synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 0.99
rpoC 767020 c.3651C>G synonymous_variant 0.12
rpoC 767023 c.3654C>T synonymous_variant 0.13
rpoC 767068 c.3699G>T synonymous_variant 0.15
rpoC 767098 c.3729T>C synonymous_variant 0.12
rpoC 767104 c.3735C>G synonymous_variant 0.1
rpoC 767105 p.Asn1246His missense_variant 0.1
rpoC 767221 c.3852C>G synonymous_variant 0.11
rpoC 767233 c.3864T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rpsL 781682 c.123T>C synonymous_variant 0.12
rpsL 781916 c.357T>C synonymous_variant 0.12
rpsL 781929 p.Gly124Ser missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.18
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.18
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.18
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.19
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.22
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.16
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.23
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.26
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.32
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.3
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.32
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.29
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.11
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.12
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.23
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.24
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.26
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.24
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.23
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.23
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.25
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.22
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.23
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.23
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.14
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.17
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.17
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.16
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.14
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.22
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.16
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.32
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.35
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.37
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.37
rrl 1475061 n.1404C>A non_coding_transcript_exon_variant 0.17
rrl 1475062 n.1405A>T non_coding_transcript_exon_variant 0.18
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.29
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.14
rrl 1475354 n.1697A>G non_coding_transcript_exon_variant 0.12
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.24
rrl 1475479 n.1822C>G non_coding_transcript_exon_variant 0.29
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.3
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.34
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.3
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.28
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.2
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.19
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.16
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.22
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.15
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.14
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.14
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.14
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.18
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.17
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.15
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.17
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.14
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.14
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.14
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.14
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.13
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.12
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.17
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.2
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.21
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.31
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.3
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.31
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.25
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.26
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.24
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.21
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.21
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.33
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.33
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.3
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.24
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.21
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.18
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.23
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.19
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.18
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.18
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.17
rpsA 1833894 p.Ala118Glu missense_variant 0.13
rpsA 1833928 c.387G>C synonymous_variant 0.12
rpsA 1833949 c.408T>C synonymous_variant 0.13
rpsA 1834348 c.807T>C synonymous_variant 0.14
rpsA 1834361 c.820T>C synonymous_variant 0.12
rpsA 1834366 c.825A>G synonymous_variant 0.1
rpsA 1834639 c.1098T>C synonymous_variant 0.12
rpsA 1834690 c.1149T>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746564 c.1035A>G synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878639 c.-132C>G upstream_gene_variant 0.17
clpC1 4038587 c.2118C>G synonymous_variant 0.12
clpC1 4038596 c.2109A>G synonymous_variant 0.13
clpC1 4038812 c.1893T>C synonymous_variant 0.11
clpC1 4038838 c.1867C>T synonymous_variant 0.15
clpC1 4038842 c.1863G>C synonymous_variant 0.15
clpC1 4038989 c.1716T>C synonymous_variant 0.13
clpC1 4038997 c.1708T>C synonymous_variant 0.14
clpC1 4039022 c.1683A>G synonymous_variant 0.19
clpC1 4039046 c.1659C>T synonymous_variant 0.18
clpC1 4039067 c.1638G>C synonymous_variant 0.14
clpC1 4039079 c.1626C>G synonymous_variant 0.13
clpC1 4039085 c.1620A>G synonymous_variant 0.14
clpC1 4039106 c.1599G>C synonymous_variant 0.11
clpC1 4039112 c.1593C>G synonymous_variant 0.14
clpC1 4039121 c.1584T>C synonymous_variant 0.11
clpC1 4039142 c.1563A>G synonymous_variant 0.12
clpC1 4039556 c.1149G>C synonymous_variant 0.12
clpC1 4039559 c.1146C>G synonymous_variant 0.11
clpC1 4039664 c.1041G>C synonymous_variant 0.12
clpC1 4039670 c.1035G>C synonymous_variant 0.12
clpC1 4039682 c.1023C>G synonymous_variant 0.11
clpC1 4039694 c.1011G>C synonymous_variant 0.11
clpC1 4039898 c.807C>G synonymous_variant 0.11
clpC1 4039931 c.774T>C synonymous_variant 0.15
clpC1 4039934 c.771G>A synonymous_variant 0.14
clpC1 4039946 c.759A>G synonymous_variant 0.15
clpC1 4039952 c.753T>C synonymous_variant 0.14
clpC1 4039955 c.750G>C synonymous_variant 0.14
clpC1 4039958 c.747G>C synonymous_variant 0.14
clpC1 4039964 c.741C>G synonymous_variant 0.16
clpC1 4039991 c.714G>C synonymous_variant 0.15
clpC1 4040021 c.684A>G synonymous_variant 0.13
clpC1 4040024 c.681A>G synonymous_variant 0.15
clpC1 4040033 c.672G>C synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0