TB-Profiler result

Run: SRR6785527
Summary

Run ID: SRR6785527

Sample name:

Date: 04-04-2023 16:02:14

Number of reads: 2855538

Percentage reads mapped: 83.2

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 6670 c.-632G>C upstream_gene_variant 0.14
gyrA 6673 c.-629A>C upstream_gene_variant 0.14
gyrA 6676 c.-626T>G upstream_gene_variant 0.14
gyrA 6700 c.-602T>C upstream_gene_variant 0.14
gyrA 6703 c.-599G>C upstream_gene_variant 0.14
gyrA 6709 c.-593A>G upstream_gene_variant 0.16
gyrA 6712 c.-590G>C upstream_gene_variant 0.15
gyrA 6728 c.-574_-572delCTAinsTTG upstream_gene_variant 0.15
gyrA 6742 c.-560A>G upstream_gene_variant 0.14
gyrA 6745 c.-557T>G upstream_gene_variant 0.14
gyrA 6751 c.-551G>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7427 c.126G>C synonymous_variant 0.14
gyrA 7442 c.141G>C synonymous_variant 0.15
gyrA 7451 c.150C>G synonymous_variant 0.16
gyrA 7457 c.156T>C synonymous_variant 0.16
gyrA 7475 c.174A>G synonymous_variant 0.13
gyrA 7480 p.Phe60Tyr missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8372 c.1071G>C synonymous_variant 0.13
gyrA 8375 c.1074G>C synonymous_variant 0.13
gyrA 8382 p.Leu361Met missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.95
mshA 575770 c.423G>A synonymous_variant 0.14
mshA 575771 p.Val142Ser missense_variant 0.14
mshA 575779 c.432A>G synonymous_variant 0.16
mshA 575782 c.435G>C synonymous_variant 0.16
mshA 575821 c.474G>C synonymous_variant 0.16
mshA 575824 c.477T>G synonymous_variant 0.19
mshA 575830 c.483C>G synonymous_variant 0.17
mshA 575833 c.486C>G synonymous_variant 0.18
mshA 575845 c.498C>T synonymous_variant 0.18
mshA 575884 c.537G>C synonymous_variant 0.14
mshA 575887 c.540G>C synonymous_variant 0.14
mshA 575907 p.Ala187Val missense_variant 0.89
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoB 760340 c.534G>T synonymous_variant 0.13
rpoB 760361 c.555T>C synonymous_variant 0.14
rpoB 760370 c.564C>G synonymous_variant 0.14
rpoB 760381 p.Thr192Met missense_variant 0.14
rpoB 760406 c.600G>C synonymous_variant 0.14
rpoB 760412 c.606C>G synonymous_variant 0.14
rpoB 760424 c.618C>G synonymous_variant 0.15
rpoB 760430 c.624T>C synonymous_variant 0.16
rpoB 760591 p.Val262Ala missense_variant 0.13
rpoB 760982 c.1176G>C synonymous_variant 0.16
rpoB 760985 c.1179G>C synonymous_variant 0.16
rpoB 760991 c.1185G>C synonymous_variant 0.16
rpoB 761006 c.1200C>G synonymous_variant 0.17
rpoB 761015 c.1209G>C synonymous_variant 0.14
rpoB 761021 c.1215G>C synonymous_variant 0.15
rpoB 761027 c.1221A>G synonymous_variant 0.17
rpoB 761036 c.1230G>C synonymous_variant 0.17
rpoB 761037 c.1231T>C synonymous_variant 0.17
rpoB 761057 c.1251G>C synonymous_variant 0.18
rpoB 761249 c.1443A>G synonymous_variant 0.14
rpoB 761306 c.1500C>G synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 763456 c.87A>G synonymous_variant 0.17
rpoC 763486 c.117T>G synonymous_variant 0.19
rpoC 763528 c.159G>A synonymous_variant 0.23
rpoC 763546 c.177A>G synonymous_variant 0.22
rpoC 763570 c.201G>C synonymous_variant 0.17
rpoC 763573 c.204G>C synonymous_variant 0.17
rpoC 763594 c.225C>T synonymous_variant 0.16
rpoC 763603 c.234C>T synonymous_variant 0.14
rpoC 763636 c.267T>C synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.19
rpoC 763675 c.306C>G synonymous_variant 0.18
rpoC 763696 c.327T>C synonymous_variant 0.2
rpoC 763702 c.333C>G synonymous_variant 0.2
rpoC 763717 c.348T>C synonymous_variant 0.23
rpoC 763723 c.354G>C synonymous_variant 0.24
rpoC 763732 c.363C>G synonymous_variant 0.25
rpoC 763741 c.372C>T synonymous_variant 0.25
rpoC 763744 c.375G>C synonymous_variant 0.26
rpoC 763765 c.396T>C synonymous_variant 0.23
rpoC 763774 c.405G>C synonymous_variant 0.24
rpoC 763807 c.438T>C synonymous_variant 0.22
rpoC 763816 c.447C>G synonymous_variant 0.2
rpoC 763835 p.Ala156Met missense_variant 0.17
rpoC 763853 p.Val162Ile missense_variant 0.16
rpoC 763858 c.489A>G synonymous_variant 0.16
rpoC 763872 p.Gly168Ala missense_variant 0.15
rpoC 763876 p.Glu169Asp missense_variant 0.14
rpoC 763879 c.510A>G synonymous_variant 0.14
rpoC 763900 c.531G>C synonymous_variant 0.14
rpoC 763991 p.Ile208Leu missense_variant 0.15
rpoC 763996 c.627T>C synonymous_variant 0.14
rpoC 764002 c.633C>G synonymous_variant 0.15
rpoC 764005 c.636G>C synonymous_variant 0.15
rpoC 764026 p.Leu219Phe missense_variant 0.14
rpoC 764112 p.Tyr248Phe missense_variant 0.14
rpoC 764116 c.747C>T synonymous_variant 0.14
rpoC 764215 c.846A>G synonymous_variant 0.16
rpoC 764236 c.867G>A synonymous_variant 0.14
rpoC 764338 c.969G>A synonymous_variant 0.16
rpoC 764353 c.984G>C synonymous_variant 0.16
rpoC 764365 c.996C>T synonymous_variant 0.15
rpoC 764381 p.Ser338Thr missense_variant 0.12
rpoC 764827 c.1458G>C synonymous_variant 0.14
rpoC 764858 c.1489T>C synonymous_variant 0.19
rpoC 764872 c.1503A>G synonymous_variant 0.2
rpoC 764888 c.1519T>C synonymous_variant 0.23
rpoC 764911 c.1542A>G synonymous_variant 0.19
rpoC 764932 c.1563C>A synonymous_variant 0.19
rpoC 764935 c.1566T>C synonymous_variant 0.19
rpoC 764948 c.1579T>C synonymous_variant 0.18
rpoC 764968 c.1599T>C synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 0.15
rpoC 765319 c.1950A>G synonymous_variant 0.13
rpoC 765421 c.2052C>G synonymous_variant 0.14
rpoC 765529 c.2160C>T synonymous_variant 0.13
rpoC 765700 c.2331T>C synonymous_variant 0.2
rpoC 765734 c.2365T>C synonymous_variant 0.18
rpoC 765739 c.2370G>T synonymous_variant 0.16
rpoC 765751 c.2382C>G synonymous_variant 0.15
rpoC 765753 p.Asp795Ala missense_variant 0.14
rpoC 765772 c.2403C>G synonymous_variant 0.15
rpoC 765784 c.2415C>G synonymous_variant 0.16
rpoC 765787 c.2418C>T synonymous_variant 0.16
rpoC 765793 c.2424C>G synonymous_variant 0.13
rpoC 765796 c.2427C>T synonymous_variant 0.14
rpoC 765811 c.2442T>C synonymous_variant 0.15
rpoC 765814 c.2445A>G synonymous_variant 0.15
rpoC 765826 c.2457T>C synonymous_variant 0.16
rpoC 765835 c.2466C>T synonymous_variant 0.15
rpoC 765850 c.2481G>C synonymous_variant 0.15
rpoC 765883 c.2514C>G synonymous_variant 0.17
rpoC 765886 c.2517C>G synonymous_variant 0.17
rpoC 765892 c.2523T>C synonymous_variant 0.17
rpoC 765937 c.2568T>C synonymous_variant 0.13
rpoC 765967 c.2598C>T synonymous_variant 0.13
rpoC 765982 c.2613C>G synonymous_variant 0.15
rpoC 765994 c.2625A>T synonymous_variant 0.13
rpoC 766010 p.Ser881Thr missense_variant 0.13
rpoC 766027 c.2658G>C synonymous_variant 0.13
rpoC 766726 c.3357T>C synonymous_variant 0.15
rpoC 766765 c.3396A>C synonymous_variant 0.16
rpoC 766774 c.3405T>C synonymous_variant 0.19
rpoC 766801 c.3432C>G synonymous_variant 0.19
rpoC 766804 c.3435A>G synonymous_variant 0.2
rpoC 766861 c.3492G>C synonymous_variant 0.17
rpoC 766864 c.3495G>C synonymous_variant 0.15
rpoC 766894 c.3525T>C synonymous_variant 0.14
rpoC 766900 c.3531T>C synonymous_variant 0.14
rpoC 766972 c.3603G>C synonymous_variant 0.14
rpoC 766996 c.3627C>T synonymous_variant 0.23
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.23
rpoC 767014 c.3645G>C synonymous_variant 0.23
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.24
rpoC 767059 c.3690T>G synonymous_variant 0.2
rpoC 767062 c.3693C>A synonymous_variant 0.22
rpoC 767098 c.3729T>C synonymous_variant 0.21
rpoC 767119 c.3750A>G synonymous_variant 0.19
rpoC 767134 c.3765C>A synonymous_variant 0.16
rpoC 767158 c.3789T>C synonymous_variant 0.16
rpoC 767180 p.Ala1271Gln missense_variant 0.15
rpoC 767191 c.3822C>G synonymous_variant 0.16
rpoC 767206 c.3837C>G synonymous_variant 0.16
rpoC 767209 c.3840T>C synonymous_variant 0.14
rpoC 767212 c.3843G>C synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 776182 p.Asp767Asn missense_variant 0.95
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781832 c.273T>C synonymous_variant 0.15
rpsL 781838 c.279G>C synonymous_variant 0.16
rpsL 781841 c.282C>G synonymous_variant 0.15
rpsL 781865 c.306G>C synonymous_variant 0.15
rpsL 781868 c.309T>C synonymous_variant 0.15
rpsL 781871 c.312G>C synonymous_variant 0.15
rpsL 781877 c.318T>C synonymous_variant 0.16
rpsL 781892 c.333A>G synonymous_variant 0.15
rpsL 781898 c.339A>T synonymous_variant 0.15
rpsL 781916 c.357T>C synonymous_variant 0.15
rplC 801367 p.Ala187Thr missense_variant 0.13
rplC 801402 c.594T>C synonymous_variant 0.17
rplC 801405 c.597T>C synonymous_variant 0.17
rplC 801423 c.615G>C synonymous_variant 0.15
rplC 801426 c.618C>G synonymous_variant 0.15
rplC 801427 p.Met207Val missense_variant 0.15
rplC 801438 c.630T>C synonymous_variant 0.15
rplC 801442 p.Ile212Val missense_variant 0.17
fbiC 1303860 c.930A>C synonymous_variant 0.13
fbiC 1303884 c.954T>G synonymous_variant 0.18
fbiC 1303905 c.975G>C synonymous_variant 0.17
fbiC 1303914 c.984C>G synonymous_variant 0.19
fbiC 1303920 c.990C>T synonymous_variant 0.17
fbiC 1303971 c.1041T>C synonymous_variant 0.15
fbiC 1303980 c.1050G>A synonymous_variant 0.17
fbiC 1303998 c.1068T>G synonymous_variant 0.17
fbiC 1304004 c.1074A>G synonymous_variant 0.15
fbiC 1304174 p.Val415Ala missense_variant 0.13
fbiC 1304184 c.1254G>C synonymous_variant 0.14
fbiC 1304187 c.1257T>C synonymous_variant 0.14
fbiC 1304208 c.1278C>T synonymous_variant 0.14
fbiC 1304893 p.Gly655Ser missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.18
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.23
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.2
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.14
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.15
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.18
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.18
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.19
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.21
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.2
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.14
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.14
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.13
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.13
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.15
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.17
rpsA 1833838 c.297G>C synonymous_variant 0.13
rpsA 1833847 c.306C>G synonymous_variant 0.19
rpsA 1833856 c.315A>G synonymous_variant 0.2
rpsA 1833874 c.333T>C synonymous_variant 0.24
rpsA 1833886 c.345C>G synonymous_variant 0.31
rpsA 1833928 c.387G>C synonymous_variant 0.28
rpsA 1833940 c.399C>G synonymous_variant 0.26
rpsA 1833971 c.430C>T synonymous_variant 0.18
rpsA 1833979 c.438T>C synonymous_variant 0.2
rpsA 1834000 c.459G>C synonymous_variant 0.19
rpsA 1834021 c.480C>T synonymous_variant 0.16
rpsA 1834030 c.489C>G synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065109 c.1081_1083delAGAinsCGC synonymous_variant 0.14
Rv2752c 3065115 c.1077C>A synonymous_variant 0.14
Rv2752c 3065142 c.1050A>C synonymous_variant 0.14
Rv2752c 3065146 p.Phe349Tyr missense_variant 0.13
Rv2752c 3065151 c.1041G>C synonymous_variant 0.15
thyX 3067391 c.555G>C synonymous_variant 0.13
thyX 3067394 c.552G>C synonymous_variant 0.13
thyX 3067439 c.507A>G synonymous_variant 0.16
thyX 3067445 c.501C>G synonymous_variant 0.16
thyX 3067457 c.489C>G synonymous_variant 0.18
thyX 3067465 p.Ile161Val missense_variant 0.2
thyX 3067475 c.471A>G synonymous_variant 0.19
thyX 3067490 c.456C>G synonymous_variant 0.16
thyX 3067493 c.453A>G synonymous_variant 0.17
thyX 3067515 p.Ser144Thr missense_variant 0.17
thyX 3067530 p.Ala139Ser missense_variant 0.17
thyX 3067545 p.Glu134Ala missense_variant 0.17
thyX 3067549 p.Thr133Ala missense_variant 0.16
thyX 3067559 c.387C>G synonymous_variant 0.13
thyX 3067781 c.165C>A synonymous_variant 0.16
thyX 3067793 c.153T>C synonymous_variant 0.16
thyX 3067799 c.147G>A synonymous_variant 0.17
thyX 3067802 c.144C>G synonymous_variant 0.19
thyX 3067814 c.132T>C synonymous_variant 0.2
thyX 3067850 c.96A>C synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877743 c.765T>C synonymous_variant 0.13
rpoA 3877764 c.744C>G synonymous_variant 0.14
rpoA 3877782 c.726T>C synonymous_variant 0.13
clpC1 4040267 c.438A>G synonymous_variant 0.16
clpC1 4040273 c.432T>C synonymous_variant 0.16
clpC1 4040277 c.427_428delTCinsAG synonymous_variant 0.16
clpC1 4040279 c.426C>G synonymous_variant 0.17
clpC1 4040291 c.414G>C synonymous_variant 0.19
clpC1 4040318 c.387C>G synonymous_variant 0.18
clpC1 4040330 c.375C>G synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embA 4244582 c.1350T>C synonymous_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.15
embB 4246556 p.Ala15Pro missense_variant 0.15
embB 4247491 c.978G>C synonymous_variant 0.14
embB 4247497 c.984T>C synonymous_variant 0.15
embB 4247512 c.999T>C synonymous_variant 0.16
aftB 4267647 p.Asp397Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408107 p.Glu32Asp missense_variant 0.95