TB-Profiler result

Run: SRR1172713

Summary

Run ID: SRR1172713

Sample name:

Date: 03-04-2023 03:08:46

Number of reads: 3278624

Percentage reads mapped: 46.19

Strain: lineage4.4

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 0.98
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288781 p.Arg154Met missense_variant 0.2 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 1.0 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 6417 p.Thr393Asn missense_variant 0.14
gyrA 7347 p.Glu16Gln missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8306 c.1005C>A synonymous_variant 0.2
gyrA 8323 p.Phe341Cys missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9394 p.Ser698Trp missense_variant 0.29
fgd1 491701 p.His307Asn missense_variant 0.2
mshA 576343 c.996C>A synonymous_variant 0.15
rpoB 760179 p.Ala125Thr missense_variant 0.4
rpoB 760280 c.474C>A synonymous_variant 0.18
rpoC 763421 p.Glu18* stop_gained 0.17
rpoC 764441 p.Ile358Val missense_variant 0.95
rpoC 764611 c.1242G>C synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.23
rpoC 764656 c.1287C>G synonymous_variant 0.11
rpoC 764745 p.Arg459Leu missense_variant 0.18
rpoC 764840 p.Ile491Val missense_variant 1.0
rpoC 765857 p.Glu830* stop_gained 0.5
rpoC 767236 p.Glu1289Asp missense_variant 0.17
rpoC 767248 p.Tyr1293* stop_gained 0.29
mmpL5 775639 p.Ile948Val missense_variant 0.96
mmpL5 776554 p.Gln643Lys missense_variant 0.29
mmpL5 776717 p.Glu588Asp missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781407 c.-153C>G upstream_gene_variant 0.2
rpsL 781627 p.Ala23Asp missense_variant 0.18
fbiC 1303024 p.Arg32Trp missense_variant 0.33
fbiC 1303276 p.Ala116Thr missense_variant 0.2
fbiC 1304711 p.Ala594Asp missense_variant 0.18
fbiC 1304715 c.1785G>T synonymous_variant 0.18
fbiC 1304737 p.Gly603Cys missense_variant 0.17
fbiC 1305058 p.Tyr710Asn missense_variant 0.18
embR 1417422 c.-75C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.56
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.67
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.5
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.5
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.5
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.25
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.2
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.18
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.2
rrs 1472340 n.495C>T non_coding_transcript_exon_variant 0.18
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.17
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.19
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.58
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.5
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.5
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.32
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.4
rrl 1474032 n.375T>C non_coding_transcript_exon_variant 0.4
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.25
rrl 1474570 n.913G>T non_coding_transcript_exon_variant 0.67
rrl 1474801 n.1145delT non_coding_transcript_exon_variant 0.29
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.33
rrl 1474828 n.1171G>C non_coding_transcript_exon_variant 0.4
rrl 1474832 n.1176delG non_coding_transcript_exon_variant 0.5
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.5
rrl 1475149 n.1492G>T non_coding_transcript_exon_variant 0.33
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.5
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.6
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.6
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.67
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.67
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.5
rrl 1476007 n.2350T>A non_coding_transcript_exon_variant 0.67
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.88
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 1.0
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.92
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.85
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.85
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.85
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.75
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.56
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.55
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.55
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.55
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
fabG1 1673229 c.-211C>A upstream_gene_variant 0.15
inhA 1674237 c.36T>G synonymous_variant 0.22
rpsA 1834705 c.1164C>G synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102086 c.957G>T synonymous_variant 0.15
ndh 2102936 p.Ala36Asp missense_variant 0.18
katG 2154443 p.Lys557Glu missense_variant 0.12
PPE35 2168191 p.Gly808Cys missense_variant 0.18
PPE35 2168270 c.2343G>C synonymous_variant 0.12
PPE35 2168691 p.Leu641Arg missense_variant 1.0
Rv1979c 2222692 c.472delG frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288754 p.Val163Ala missense_variant 0.29
pncA 2289118 p.His42Asn missense_variant 0.25
pncA 2289626 c.-385G>A upstream_gene_variant 0.17
ahpC 2726204 c.12A>C synonymous_variant 0.18
ahpC 2726363 p.Phe57Leu missense_variant 0.2
folC 2746949 p.Ala217Glu missense_variant 0.23
pepQ 2859967 p.Asp151Gly missense_variant 1.0
pepQ 2860015 p.Lys135Thr missense_variant 0.12
ribD 2986771 c.-68C>A upstream_gene_variant 0.29
ribD 2987598 p.Arg254Ser missense_variant 0.33
Rv2752c 3065715 c.477T>C synonymous_variant 1.0
Rv2752c 3066203 c.-12G>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086901 p.Arg28Ser missense_variant 0.33
ald 3086916 p.Val33Met missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568635 p.Leu15Phe missense_variant 0.25
whiB7 3568685 c.-6C>T upstream_gene_variant 0.22
fbiB 3640758 c.-777G>T upstream_gene_variant 0.22
alr 3840637 p.Pro262Thr missense_variant 0.22
ddn 3986935 p.Arg31His missense_variant 0.22
clpC1 4039900 p.Leu269Ile missense_variant 0.29
clpC1 4039931 c.774T>A synonymous_variant 0.2
clpC1 4040678 c.27C>A synonymous_variant 0.22
panD 4044237 c.45G>T synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245088 p.Ser619* stop_gained 0.22
embA 4245765 p.Glu845* stop_gained 0.23
embA 4246367 p.Tyr1045* stop_gained 0.17
embB 4247947 c.1434G>A synonymous_variant 1.0
embB 4248035 p.Val508Ile missense_variant 0.29
embB 4248131 p.Arg540Ser missense_variant 0.15
aftB 4268523 p.Leu105Trp missense_variant 0.13
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
ubiA 4268948 p.Gly296Trp missense_variant 0.17
ubiA 4269124 p.Ala237Val missense_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ubiA 4269662 p.Ala58Ser missense_variant 0.17
ubiA 4269862 c.-29G>A upstream_gene_variant 0.22
ubiA 4269892 c.-59G>T upstream_gene_variant 0.15
ubiA 4269934 c.-101C>A upstream_gene_variant 0.25
ubiA 4269946 c.-113G>T upstream_gene_variant 0.5
ethA 4326181 p.Phe431Leu missense_variant 0.22
ethA 4326205 c.1269C>A synonymous_variant 0.15
ethA 4326719 p.Ala252Phe missense_variant 1.0
ethA 4327547 c.-74C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0