TB-Profiler result

Run: SRR6046239
Summary

Run ID: SRR6046239

Sample name:

Date: 04-04-2023 12:13:27

Number of reads: 59740

Percentage reads mapped: 14.29

Strain: lineage4.9;lineage3

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
lineage3 East-African-Indian CAS RD750 0.11
lineage4 Euro-American LAM;T;S;X;H None 0.96
lineage4.9 Euro-American (H37Rv-like) T1 None 0.88
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 0.82 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.75 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
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 5570 p.Ser111Thr missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620384 p.Pro165Leu missense_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761194 p.Gly463Glu missense_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1472180 n.335A>T non_coding_transcript_exon_variant 0.5
rrs 1472181 n.336G>T non_coding_transcript_exon_variant 0.5
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.75
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.8
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.8
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.8
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.8
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.7
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.8
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.6
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.67
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.3
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.89
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.81
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.82
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.7
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.87
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.13
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.87
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.2
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.87
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.69
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.89
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.84
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.82
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.81
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.14
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.83
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.75
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.6
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.6
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.6
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.8
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.8
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.8
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.6
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.6
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.67
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.67
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.67
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.75
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.75
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 1.0
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 1.0
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 1.0
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 1.0
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 1.0
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 1.0
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 1.0
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 1.0
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 1.0
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 1.0
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 1.0
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.6
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.6
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.8
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.6
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.6
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.5
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.5
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.25
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.29
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.33
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.33
rrl 1474658 n.1001A>G non_coding_transcript_exon_variant 0.29
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.29
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.29
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.33
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.33
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.67
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 1.0
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 1.0
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 1.0
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 1.0
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 1.0
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 1.0
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 1.0
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 1.0
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 1.0
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.25
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.25
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.33
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.33
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.67
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.67
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 1.0
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 1.0
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 1.0
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 1.0
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 1.0
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.75
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.83
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.83
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 1.0
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 1.0
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 1.0
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.75
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.8
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.83
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.89
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.89
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.9
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.82
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.94
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.79
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.93
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.78
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726114 c.-79C>T upstream_gene_variant 1.0
thyA 3074112 c.360C>T synonymous_variant 0.67
thyA 3074123 p.Asp117His missense_variant 0.67
thyA 3074126 c.346C>T synonymous_variant 0.67
thyA 3074130 c.342G>T synonymous_variant 0.67
thyA 3074159 p.Ser105Thr missense_variant 0.67
thyA 3074160 c.312A>G synonymous_variant 0.5
thyA 3074163 p.Ala103Thr missense_variant 0.75
thyA 3074166 c.306G>C synonymous_variant 0.5
thyA 3074172 c.300G>C synonymous_variant 0.5
thyA 3074181 c.291A>G synonymous_variant 0.67
thyA 3074184 c.288A>G synonymous_variant 0.67
thyA 3074187 c.285T>C synonymous_variant 0.67
thyA 3074193 p.Ile93Val missense_variant 0.67
thyA 3074205 p.Glu89Asp missense_variant 0.5
thyA 3074208 c.264C>G synonymous_variant 0.5
thyA 3074211 c.261A>T synonymous_variant 0.5
thyA 3074214 c.258T>C synonymous_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339228 c.111C>T synonymous_variant 0.67
alr 3841473 c.-53G>A upstream_gene_variant 1.0
alr 3841614 c.-194C>T upstream_gene_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 1.0
aftB 4268976 c.-140G>C upstream_gene_variant 0.67
ubiA 4268982 p.Leu284Phe missense_variant 0.67
aftB 4268985 c.-149A>G upstream_gene_variant 0.67
ubiA 4269001 p.Ala278Val missense_variant 0.67
aftB 4269006 c.-170T>C upstream_gene_variant 0.67
aftB 4269009 c.-173A>G upstream_gene_variant 0.67
aftB 4269012 c.-176G>C upstream_gene_variant 0.67
aftB 4269027 c.-191C>G upstream_gene_variant 0.67
aftB 4269033 c.-197T>C upstream_gene_variant 0.67
aftB 4269036 c.-200C>G upstream_gene_variant 0.67
aftB 4269042 c.-206G>C upstream_gene_variant 0.67
ubiA 4269860 c.-27C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0