TB-Profiler result

Run: SRR1173521
Summary

Run ID: SRR1173521

Sample name:

Date: 03-04-2023 03:26:37

Number of reads: 182555

Percentage reads mapped: 1.76

Strain: lineage4.9

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.94
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 1472733 n.888G>A non_coding_transcript_exon_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid
katG 2155192 p.Gly307Glu missense_variant 0.5 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrB 6524 p.Arg429Ser missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8544 p.Asp415Tyr missense_variant 0.5
gyrA 8597 c.1296C>A synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490861 p.Ala27Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.5
mshA 576128 p.Leu261Ile missense_variant 0.67
ccsA 619694 c.-197C>A upstream_gene_variant 1.0
ccsA 620402 p.Trp171Leu missense_variant 1.0
ccsA 620499 c.609G>T synonymous_variant 0.67
ccsA 620544 c.654G>T synonymous_variant 1.0
rpoB 761752 p.Ala649Asp missense_variant 0.4
rpoB 762522 p.Pro906Thr missense_variant 0.33
rpoB 762774 p.Arg990Ser missense_variant 0.5
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766219 p.Asp950Glu missense_variant 0.29
rpoC 766223 c.2854C>T synonymous_variant 0.29
rpoC 766230 p.Ala954Asp missense_variant 0.29
rpoC 767092 c.3723C>T synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776766 p.Ala572Val missense_variant 0.29
mmpL5 777635 c.846C>A synonymous_variant 0.4
mmpL5 778992 c.-512C>A upstream_gene_variant 0.2
mmpR5 779006 p.Gly6Val missense_variant 0.22
mmpR5 779186 p.Gly66Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801330 c.522G>T synonymous_variant 0.67
fbiC 1302975 c.45C>A synonymous_variant 1.0
fbiC 1303001 p.Ser24* stop_gained 1.0
fbiC 1304866 p.Gly646Trp missense_variant 1.0
fbiC 1304878 p.Arg650Cys missense_variant 1.0
fbiC 1304910 c.1980G>T synonymous_variant 0.5
embR 1417373 c.-26G>A upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471878 n.33C>T non_coding_transcript_exon_variant 0.4
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.4
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.29
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.64
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.64
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.64
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.64
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.8
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.8
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.8
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.8
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.79
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.84
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.84
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.8
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.62
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.95
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.99
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.99
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.99
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.99
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.99
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.98
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.99
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.99
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.98
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.98
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.97
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.96
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.88
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.94
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.94
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.96
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.95
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.96
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.97
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.98
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.98
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.99
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.99
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.97
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.97
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.96
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.78
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.5
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.47
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.4
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.78
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.78
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.78
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.78
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.75
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.8
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.7
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.72
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.72
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.72
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.72
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.74
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.74
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.74
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.74
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.79
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.87
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.93
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.93
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.3
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.27
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.27
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.27
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.36
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.27
rrs 1473287 n.1442C>A non_coding_transcript_exon_variant 0.31
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.17
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.43
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.4
rrl 1474128 n.471G>T non_coding_transcript_exon_variant 0.33
rrl 1474198 n.541G>T non_coding_transcript_exon_variant 0.33
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.22
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.33
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.5
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.43
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.75
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.75
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.75
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.75
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.75
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.75
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.82
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.82
rrl 1474848 n.1191G>A non_coding_transcript_exon_variant 0.9
rrl 1474862 n.1205C>T non_coding_transcript_exon_variant 0.9
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 1.0
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 1.0
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 1.0
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 1.0
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 1.0
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.75
rrl 1475534 n.1877G>T non_coding_transcript_exon_variant 0.2
rrl 1475613 n.1956A>T non_coding_transcript_exon_variant 0.2
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.67
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 0.67
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.67
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.5
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.4
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.4
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.87
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.83
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.83
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.85
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.85
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.85
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.85
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.73
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.22
rrl 1475961 n.2304C>T non_coding_transcript_exon_variant 0.29
rrl 1476131 n.2474C>A non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.43
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.43
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.67
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.67
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.5
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.5
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.6
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.5
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.8
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.8
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.89
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.99
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.99
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 1.0
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 1.0
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.99
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.99
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.99
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.99
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.99
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.96
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.92
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.88
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.74
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.64
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.6
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.43
rrl 1476565 n.2908G>T non_coding_transcript_exon_variant 0.33
rrl 1476568 n.2911G>A non_coding_transcript_exon_variant 0.33
rrl 1476599 n.2942C>T non_coding_transcript_exon_variant 0.67
inhA 1673366 c.-836G>A upstream_gene_variant 0.5
fabG1 1673891 p.Ala151Asp missense_variant 0.33
inhA 1674953 p.Pro251Leu missense_variant 0.67
rpsA 1834856 p.Glu439Lys missense_variant 0.5
tlyA 1917904 c.-36C>T upstream_gene_variant 0.4
ndh 2102438 p.Arg202Leu missense_variant 1.0
katG 2154077 p.Gln679* stop_gained 0.5
katG 2154588 c.1524C>T synonymous_variant 1.0
katG 2154996 c.1116G>T synonymous_variant 1.0
katG 2156268 c.-157G>T upstream_gene_variant 0.5
PPE35 2168736 p.Ser626Ile missense_variant 0.4
PPE35 2169101 c.1512G>A synonymous_variant 0.5
PPE35 2169677 c.936C>A synonymous_variant 0.18
PPE35 2169852 p.Gly254Val missense_variant 0.4
Rv1979c 2221731 c.1434G>A synonymous_variant 0.33
Rv1979c 2221778 p.Ala463Ser missense_variant 0.22
Rv1979c 2221843 p.Arg441Leu missense_variant 0.33
Rv1979c 2221940 c.1225C>A synonymous_variant 1.0
Rv1979c 2222036 p.Leu377Met missense_variant 0.4
Rv1979c 2222082 c.1083C>A synonymous_variant 0.22
Rv1979c 2222313 c.852G>A synonymous_variant 0.25
Rv1979c 2223253 c.-89C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223305 c.-141G>T upstream_gene_variant 0.4
pncA 2288804 c.438G>T synonymous_variant 1.0
pncA 2289995 c.-754C>A upstream_gene_variant 0.67
pncA 2290048 c.-807C>A upstream_gene_variant 0.67
kasA 2519218 c.1104G>T synonymous_variant 0.5
folC 2746482 c.1117C>A synonymous_variant 1.0
folC 2746647 p.Gln318Lys missense_variant 0.67
pepQ 2859524 p.Gly299Cys missense_variant 0.29
pepQ 2860306 p.Gly38Val missense_variant 0.5
thyA 3073758 p.Ile238Met missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086879 c.60G>A synonymous_variant 0.67
ald 3087356 c.537C>T synonymous_variant 0.5
ald 3087598 p.Pro260Gln missense_variant 1.0
fprA 3473955 c.-52G>T upstream_gene_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612635 p.Ala161Glu missense_variant 0.4
fbiB 3642382 p.Ala283Asp missense_variant 1.0
rpoA 3878043 c.465G>T synonymous_variant 0.33
rpoA 3878276 p.Leu78Met missense_variant 0.67
ddn 3986841 c.-3G>T upstream_gene_variant 0.4
ddn 3987084 p.Gly81Cys missense_variant 0.5
panD 4044113 c.168delC frameshift_variant 0.25
panD 4044216 p.Tyr22* stop_gained 0.4
panD 4044377 c.-96G>T upstream_gene_variant 0.67
panD 4044397 c.-116G>T upstream_gene_variant 0.5
panD 4044438 c.-157G>T upstream_gene_variant 0.5
embC 4240446 p.Pro195Gln missense_variant 0.67
embC 4242233 p.Pro791Ser missense_variant 1.0
embC 4242273 p.Gly804Val missense_variant 0.5
embC 4242633 p.Pro924Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242776 p.Gln972Lys missense_variant 0.67
embA 4244076 c.844C>A synonymous_variant 1.0
embA 4244384 c.1152G>T synonymous_variant 0.33
embB 4249183 c.2670C>T synonymous_variant 0.67
embB 4249375 c.2862G>T synonymous_variant 1.0
embB 4249496 p.Pro995Thr missense_variant 1.0
aftB 4267701 p.Trp379Leu missense_variant 1.0
aftB 4267729 p.Trp370Arg missense_variant 1.0
aftB 4267731 p.Arg369Leu missense_variant 1.0
aftB 4267880 c.957C>A synonymous_variant 1.0
aftB 4268096 c.741C>A synonymous_variant 0.4
aftB 4268137 p.Leu234Met missense_variant 0.4
ubiA 4269722 p.Ala38Thr missense_variant 0.67
ethA 4326758 p.Arg239Gln missense_variant 1.0
ethR 4327321 c.-228G>A upstream_gene_variant 0.67
ethA 4327830 c.-357G>T upstream_gene_variant 0.5
ethA 4328222 c.-749G>A upstream_gene_variant 0.67
whiB6 4338243 c.279C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0