TB-Profiler result

Run: SRR5341408
Summary

Run ID: SRR5341408

Sample name:

Date: 04-04-2023 10:19:52

Number of reads: 793132

Percentage reads mapped: 84.84

Strain: lineage3

Drug-resistance: Sensitive

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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 0.99
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
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 6362 c.-940T>C upstream_gene_variant 0.16
gyrA 6367 c.-935C>T upstream_gene_variant 0.12
gyrA 6379 c.-923C>G upstream_gene_variant 0.12
gyrA 6382 c.-920A>G upstream_gene_variant 0.12
gyrA 6388 c.-914T>C upstream_gene_variant 0.12
gyrB 6398 p.Val387Ile missense_variant 0.11
gyrA 6523 c.-779G>C upstream_gene_variant 0.12
gyrA 6526 c.-776T>C upstream_gene_variant 0.12
gyrA 6538 c.-764C>G upstream_gene_variant 0.13
gyrA 6547 c.-755T>C upstream_gene_variant 0.14
gyrA 6550 c.-752A>G upstream_gene_variant 0.14
gyrA 6551 c.-751T>C upstream_gene_variant 0.14
gyrA 6568 c.-734C>G upstream_gene_variant 0.15
gyrA 6571 c.-731T>C upstream_gene_variant 0.15
gyrA 6577 c.-725T>C upstream_gene_variant 0.14
gyrA 6583 c.-719G>C upstream_gene_variant 0.13
gyrA 6586 c.-716T>C upstream_gene_variant 0.14
gyrA 6589 c.-713G>A upstream_gene_variant 0.14
gyrA 6598 c.-704C>G upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7514 c.213C>G synonymous_variant 0.13
gyrA 7523 c.222C>A synonymous_variant 0.13
gyrA 7526 c.225G>A synonymous_variant 0.13
gyrA 7532 c.231T>C synonymous_variant 0.12
gyrA 7541 c.240C>G synonymous_variant 0.12
gyrA 7569 p.Ala90Ser missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8414 c.1113C>T synonymous_variant 0.12
gyrA 8420 c.1119T>C synonymous_variant 0.12
gyrA 8432 c.1131C>G synonymous_variant 0.15
gyrA 8453 c.1152A>C synonymous_variant 0.16
gyrA 8471 c.1170T>C synonymous_variant 0.11
gyrA 8579 c.1278C>T synonymous_variant 0.12
gyrA 8597 c.1296C>G synonymous_variant 0.14
gyrA 8603 c.1302A>C synonymous_variant 0.14
gyrA 8609 c.1308G>C synonymous_variant 0.14
gyrA 8612 c.1311C>T synonymous_variant 0.15
gyrA 8619 c.1318T>C synonymous_variant 0.15
gyrA 8624 c.1323G>C synonymous_variant 0.2
gyrA 8627 c.1326C>G synonymous_variant 0.2
gyrA 8630 c.1329G>C synonymous_variant 0.2
gyrA 8636 c.1335A>C synonymous_variant 0.23
gyrA 8642 c.1341A>G synonymous_variant 0.23
gyrA 8645 c.1344C>T synonymous_variant 0.23
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491550 c.768T>C synonymous_variant 0.11
fgd1 491569 p.Asp263Asn missense_variant 0.11
fgd1 491577 c.795G>C synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760181 c.375T>G synonymous_variant 0.11
rpoB 760454 c.648C>G synonymous_variant 0.17
rpoB 760463 c.657C>T synonymous_variant 0.17
rpoB 760475 c.669A>G synonymous_variant 0.12
rpoB 760478 c.672C>T synonymous_variant 0.12
rpoB 760481 c.675G>T synonymous_variant 0.12
rpoB 760484 c.678A>G synonymous_variant 0.11
rpoB 760487 c.681G>C synonymous_variant 0.12
rpoB 760508 c.702G>A synonymous_variant 0.14
rpoB 760532 c.726T>C synonymous_variant 0.11
rpoB 760535 c.729C>G synonymous_variant 0.12
rpoB 760634 c.828T>C synonymous_variant 0.12
rpoB 760646 c.840C>G synonymous_variant 0.11
rpoB 761015 c.1209G>C synonymous_variant 0.12
rpoB 761027 c.1221A>G synonymous_variant 0.16
rpoB 761036 c.1230G>C synonymous_variant 0.16
rpoB 761037 c.1231T>C synonymous_variant 0.16
rpoB 761051 c.1245G>T synonymous_variant 0.14
rpoB 761054 c.1248G>C synonymous_variant 0.14
rpoB 761057 c.1251G>C synonymous_variant 0.14
rpoB 761060 c.1254C>G synonymous_variant 0.14
rpoB 761063 c.1257C>G synonymous_variant 0.16
rpoB 761066 c.1260G>C synonymous_variant 0.16
rpoB 761096 c.1290G>C synonymous_variant 0.12
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.12
rpoB 761102 c.1296A>G synonymous_variant 0.12
rpoB 761204 c.1398C>G synonymous_variant 0.15
rpoB 761217 p.Pro471Ser missense_variant 0.14
rpoB 761220 c.1414_1416delTCGinsAGC synonymous_variant 0.15
rpoB 761234 c.1428G>C synonymous_variant 0.15
rpoB 761249 c.1443A>G synonymous_variant 0.25
rpoB 761252 c.1446C>G synonymous_variant 0.25
rpoB 761255 c.1449T>G synonymous_variant 0.25
rpoB 761258 c.1452G>A synonymous_variant 0.22
rpoB 761261 c.1455G>C synonymous_variant 0.2
rpoB 761264 c.1458C>G synonymous_variant 0.2
rpoB 761273 c.1467T>C synonymous_variant 0.17
rpoB 762140 c.2334G>C synonymous_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.12
rpoB 762149 c.2343G>C synonymous_variant 0.12
rpoB 762158 c.2352G>T synonymous_variant 0.12
rpoB 762167 c.2361T>C synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762905 p.Asp1033Glu missense_variant 0.11
rpoC 762983 c.-387C>T upstream_gene_variant 0.12
rpoC 762989 c.-381G>A upstream_gene_variant 0.12
rpoC 762995 c.-375G>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763468 c.99G>C synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.25
rpoC 763570 c.201G>T synonymous_variant 0.25
rpoC 763573 c.204G>C synonymous_variant 0.25
rpoC 763615 c.246G>C synonymous_variant 0.18
rpoC 763618 c.249C>T synonymous_variant 0.18
rpoC 763660 c.291T>G synonymous_variant 0.12
rpoC 763702 c.333C>G synonymous_variant 0.17
rpoC 763708 c.339G>T synonymous_variant 0.17
rpoC 763714 c.345G>C synonymous_variant 0.18
rpoC 763717 c.348T>C synonymous_variant 0.19
rpoC 763723 c.354G>C synonymous_variant 0.21
rpoC 763732 c.363C>G synonymous_variant 0.21
rpoC 763735 c.366G>A synonymous_variant 0.21
rpoC 763741 c.372C>T synonymous_variant 0.19
rpoC 763744 c.375G>C synonymous_variant 0.18
rpoC 763765 c.396T>G synonymous_variant 0.2
rpoC 763781 p.Ser138Ala missense_variant 0.11
rpoC 763801 c.432C>G synonymous_variant 0.14
rpoC 764626 c.1257C>T synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764668 c.1299C>T synonymous_variant 0.16
rpoC 764764 c.1395T>C synonymous_variant 0.12
rpoC 764791 c.1422C>G synonymous_variant 0.15
rpoC 764797 c.1428G>C synonymous_variant 0.13
rpoC 764803 c.1434C>T synonymous_variant 0.13
rpoC 764809 c.1440C>T synonymous_variant 0.14
rpoC 764815 c.1446A>G synonymous_variant 0.14
rpoC 764827 c.1458G>C synonymous_variant 0.17
rpoC 764844 p.Ala492Gly missense_variant 0.13
rpoC 764858 c.1489T>C synonymous_variant 0.12
rpoC 765754 p.Asp795Glu missense_variant 0.11
rpoC 765802 p.Phe811Leu missense_variant 0.11
rpoC 765823 c.2454C>G synonymous_variant 0.11
rpoC 765826 c.2457T>C synonymous_variant 0.12
rpoC 765835 c.2466C>T synonymous_variant 0.12
rpoC 765875 p.Val836Ile missense_variant 0.15
rpoC 765886 c.2517C>G synonymous_variant 0.15
rpoC 765904 c.2535C>G synonymous_variant 0.12
rpoC 766345 c.2976T>C synonymous_variant 0.2
rpoC 766348 c.2979A>G synonymous_variant 0.25
rpoC 766351 c.2982C>G synonymous_variant 0.22
rpoC 766369 c.3000C>G synonymous_variant 0.17
rpoC 766384 c.3015A>G synonymous_variant 0.12
rpoC 766393 c.3024C>G synonymous_variant 0.11
rpoC 767020 c.3651C>G synonymous_variant 0.12
rpoC 767098 c.3729T>C synonymous_variant 0.1
rpoC 767167 c.3798C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776030 c.2451G>T synonymous_variant 0.22
mmpL5 776039 c.2442C>G synonymous_variant 0.17
mmpL5 776075 c.2406C>G synonymous_variant 0.17
mmpL5 776078 c.2403C>T synonymous_variant 0.17
mmpL5 776087 c.2394C>T synonymous_variant 0.15
mmpL5 776093 c.2386_2388delCGCinsAGA synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776107 c.2374C>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781718 c.159C>G synonymous_variant 0.12
rpsL 781724 c.165G>C synonymous_variant 0.12
rpsL 781728 c.169T>C synonymous_variant 0.12
rpsL 781733 c.174G>C synonymous_variant 0.13
rpsL 781736 c.177T>C synonymous_variant 0.12
rpsL 781742 c.183C>T synonymous_variant 0.14
rplC 800690 c.-119C>T upstream_gene_variant 0.13
rplC 800693 c.-116A>G upstream_gene_variant 0.12
rplC 800703 c.-106T>C upstream_gene_variant 0.12
fbiC 1303545 c.615A>G synonymous_variant 0.14
fbiC 1303581 c.651G>C synonymous_variant 0.2
fbiC 1303584 c.654C>G synonymous_variant 0.22
fbiC 1303590 c.660A>G synonymous_variant 0.22
fbiC 1303602 c.672A>G synonymous_variant 0.15
fbiC 1303611 c.681G>T synonymous_variant 0.14
fbiC 1303614 c.684C>G synonymous_variant 0.14
fbiC 1303632 c.702T>G synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.12
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.12
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.14
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.12
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.12
rrs 1472973 n.1128A>C non_coding_transcript_exon_variant 0.21
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.16
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 1473276 n.1431A>G non_coding_transcript_exon_variant 0.25
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.19
rrl 1473696 n.39T>C non_coding_transcript_exon_variant 0.19
rrl 1473697 n.40C>T non_coding_transcript_exon_variant 0.19
rrl 1473699 n.42A>G non_coding_transcript_exon_variant 0.2
rrl 1473728 n.71A>T non_coding_transcript_exon_variant 0.15
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.18
rrl 1474057 n.400G>T non_coding_transcript_exon_variant 0.12
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.24
rrl 1474293 n.637_647delCCTCTCCGGAG non_coding_transcript_exon_variant 0.21
rrl 1474306 n.649A>T non_coding_transcript_exon_variant 0.18
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.16
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.16
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.13
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.23
rrl 1474629 n.972G>A non_coding_transcript_exon_variant 0.22
rrl 1474631 n.974G>T non_coding_transcript_exon_variant 0.22
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.21
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.21
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.21
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.21
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.21
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.21
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.21
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.29
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.23
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.31
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.12
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.19
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.25
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.26
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.25
rrl 1476032 n.2375C>T non_coding_transcript_exon_variant 0.17
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.17
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.17
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.17
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.15
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.16
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.14
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.17
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.18
rrl 1476105 n.2448G>T non_coding_transcript_exon_variant 0.19
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.19
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.19
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.26
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.3
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.27
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.19
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.26
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.32
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.32
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.3
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.21
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.15
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.14
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.13
rpsA 1833616 c.75A>C synonymous_variant 0.12
rpsA 1833619 c.78A>C synonymous_variant 0.12
rpsA 1833628 c.87G>C synonymous_variant 0.11
rpsA 1833787 c.246C>G synonymous_variant 0.12
rpsA 1833790 c.249T>C synonymous_variant 0.12
rpsA 1833793 c.252C>T synonymous_variant 0.12
rpsA 1833811 c.270G>C synonymous_variant 0.1
rpsA 1833829 c.288A>G synonymous_variant 0.14
rpsA 1833838 c.297G>C synonymous_variant 0.13
rpsA 1833841 c.300C>G synonymous_variant 0.13
rpsA 1833847 c.306C>G synonymous_variant 0.13
rpsA 1833970 c.429G>C synonymous_variant 0.11
rpsA 1834361 c.820T>C synonymous_variant 0.12
rpsA 1834366 c.825A>G synonymous_variant 0.14
rpsA 1834489 c.948T>C synonymous_variant 0.11
rpsA 1834520 p.Ala327Ser missense_variant 0.12
rpsA 1834528 c.987T>C synonymous_variant 0.12
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 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518249 c.135A>C synonymous_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746519 c.1080T>C synonymous_variant 0.18
Rv2752c 3067152 c.-961G>A upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087811 p.Ala331Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641463 c.-72G>T upstream_gene_variant 0.13
rpoA 3877734 c.774G>T synonymous_variant 0.12
rpoA 3877737 c.771G>C synonymous_variant 0.12
rpoA 3878358 c.150C>G synonymous_variant 0.13
rpoA 3878364 c.144A>C synonymous_variant 0.13
rpoA 3878388 c.120C>G synonymous_variant 0.15
rpoA 3878391 c.117T>G synonymous_variant 0.17
rpoA 3878394 c.114G>T synonymous_variant 0.17
rpoA 3878406 c.102G>T synonymous_variant 0.17
rpoA 3878415 c.93C>T synonymous_variant 0.17
rpoA 3878424 c.84G>C synonymous_variant 0.17
clpC1 4039205 c.1500C>T synonymous_variant 0.16
clpC1 4039241 c.1464G>C synonymous_variant 0.12
clpC1 4039262 c.1443C>T synonymous_variant 0.12
clpC1 4039271 c.1434G>A synonymous_variant 0.11
clpC1 4039274 c.1431G>C synonymous_variant 0.11
clpC1 4039280 c.1425G>C synonymous_variant 0.11
clpC1 4039556 c.1149G>C synonymous_variant 0.13
clpC1 4039559 c.1146C>G synonymous_variant 0.13
clpC1 4039568 p.Met379Ile missense_variant 0.13
clpC1 4039574 p.Ala377Pro missense_variant 0.13
clpC1 4039592 c.1113G>C synonymous_variant 0.13
clpC1 4039613 c.1092C>T synonymous_variant 0.12
clpC1 4039616 c.1089G>C synonymous_variant 0.12
clpC1 4039622 c.1083C>A synonymous_variant 0.12
clpC1 4039850 c.855T>C synonymous_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0