TB-Profiler result

Run: ERR6326069
Summary

Run ID: ERR6326069

Sample name:

Date: 02-04-2023 01:58:47

Number of reads: 5210490

Percentage reads mapped: 89.17

Strain: lineage4.3.4.1

Drug-resistance: Pre-XDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 1.0
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
gyrA 7582 p.Asp94Ala missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.87 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp 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
gyrA 6841 c.-461T>C upstream_gene_variant 0.14
gyrA 6844 c.-458T>G upstream_gene_variant 0.14
gyrA 6853 c.-449A>G upstream_gene_variant 0.14
gyrA 6856 c.-446T>C upstream_gene_variant 0.14
gyrA 6862 c.-440C>G upstream_gene_variant 0.14
gyrA 6878 c.-424T>C upstream_gene_variant 0.14
gyrA 6881 c.-421T>C upstream_gene_variant 0.15
gyrA 6904 c.-398C>G upstream_gene_variant 0.14
gyrA 6910 c.-392G>A upstream_gene_variant 0.14
gyrB 6911 p.Asn558His missense_variant 0.14
gyrA 6919 c.-383T>C upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8225 c.924T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9315 c.2014C>T synonymous_variant 0.95
mshA 576113 p.Arg256Gly missense_variant 0.31
ccsA 620349 c.459A>G synonymous_variant 0.15
ccsA 620362 p.Ala158Thr missense_variant 0.14
rpoB 760283 c.477G>C synonymous_variant 0.15
rpoB 760307 c.501T>C synonymous_variant 0.17
rpoB 760328 c.522G>C synonymous_variant 0.17
rpoB 760331 c.525G>C synonymous_variant 0.18
rpoB 760337 c.531C>G synonymous_variant 0.19
rpoB 760340 c.534G>C synonymous_variant 0.19
rpoB 760361 c.555T>C synonymous_variant 0.18
rpoB 760376 p.Asp190Glu missense_variant 0.17
rpoB 760406 c.600G>C synonymous_variant 0.17
rpoB 760418 c.612G>C synonymous_variant 0.17
rpoB 760424 c.618C>G synonymous_variant 0.17
rpoB 760430 c.624T>C synonymous_variant 0.17
rpoB 760475 c.669A>G synonymous_variant 0.17
rpoB 760481 c.675G>C synonymous_variant 0.17
rpoB 760484 c.678A>G synonymous_variant 0.16
rpoB 760522 p.Ser239Asn missense_variant 0.16
rpoB 760532 c.726T>C synonymous_variant 0.16
rpoB 760533 p.Val243Thr missense_variant 0.15
rpoB 760547 c.741G>C synonymous_variant 0.18
rpoB 760563 p.Arg253Met missense_variant 0.18
rpoB 760591 p.Val262Ala missense_variant 0.2
rpoB 760611 c.805T>C synonymous_variant 0.18
rpoB 760634 c.828T>C synonymous_variant 0.14
rpoB 760646 c.840C>G synonymous_variant 0.15
rpoB 760655 c.849A>G synonymous_variant 0.15
rpoB 760661 c.855A>C synonymous_variant 0.14
rpoB 760793 c.987A>G synonymous_variant 0.15
rpoB 760805 c.999G>C synonymous_variant 0.17
rpoB 760817 c.1011A>G synonymous_variant 0.17
rpoB 760820 c.1014T>C synonymous_variant 0.17
rpoB 760826 c.1020C>G synonymous_variant 0.19
rpoB 760830 c.1024T>C synonymous_variant 0.18
rpoB 760845 p.Thr347Pro missense_variant 0.2
rpoB 760859 c.1053T>C synonymous_variant 0.22
rpoB 760862 c.1056G>C synonymous_variant 0.2
rpoB 760869 p.Val355Ile missense_variant 0.21
rpoB 760886 c.1080A>G synonymous_variant 0.19
rpoB 760919 c.1113C>G synonymous_variant 0.19
rpoB 760925 c.1119T>C synonymous_variant 0.18
rpoB 760928 c.1122G>C synonymous_variant 0.17
rpoB 760934 c.1128C>T synonymous_variant 0.16
rpoB 760970 c.1164G>C synonymous_variant 0.15
rpoB 760982 c.1176G>C synonymous_variant 0.14
rpoB 760985 c.1179G>C synonymous_variant 0.14
rpoB 761261 c.1455G>T synonymous_variant 0.14
rpoB 761297 c.1491C>T synonymous_variant 0.14
rpoB 761570 c.1764T>C synonymous_variant 0.14
rpoB 761606 c.1800C>G synonymous_variant 0.14
rpoB 761873 c.2067A>G synonymous_variant 0.14
rpoB 761885 c.2079T>C synonymous_variant 0.14
rpoB 762014 c.2208C>T synonymous_variant 0.13
rpoC 763028 c.-342T>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>G upstream_gene_variant 0.14
rpoC 763034 c.-336C>G upstream_gene_variant 0.14
rpoC 763040 c.-330C>G upstream_gene_variant 0.15
rpoC 763070 c.-300T>C upstream_gene_variant 0.2
rpoC 763076 c.-294C>G upstream_gene_variant 0.22
rpoC 763085 c.-285C>G upstream_gene_variant 0.22
rpoC 763115 c.-255T>C upstream_gene_variant 0.2
rpoC 763136 c.-234C>T upstream_gene_variant 0.23
rpoC 763148 c.-222G>C upstream_gene_variant 0.22
rpoC 763158 c.-212C>T upstream_gene_variant 0.22
rpoC 763166 c.-204A>G upstream_gene_variant 0.21
rpoC 763169 c.-201A>G upstream_gene_variant 0.21
rpoC 763206 c.-164_-162delAGTinsTCC upstream_gene_variant 0.14
rpoC 763642 c.273G>C synonymous_variant 0.14
rpoC 763658 p.Leu97Phe missense_variant 0.15
rpoC 764005 c.636G>C synonymous_variant 0.14
rpoC 764011 c.642T>C synonymous_variant 0.13
rpoC 764083 c.714A>G synonymous_variant 0.15
rpoC 764098 c.729A>G synonymous_variant 0.15
rpoC 764101 c.732C>G synonymous_variant 0.15
rpoC 764110 c.741C>T synonymous_variant 0.17
rpoC 764131 c.762T>C synonymous_variant 0.18
rpoC 764161 c.792G>C synonymous_variant 0.14
rpoC 764195 p.Ser276Gln missense_variant 0.15
rpoC 764203 c.834G>T synonymous_variant 0.16
rpoC 764206 c.837T>C synonymous_variant 0.16
rpoC 764257 c.888G>C synonymous_variant 0.18
rpoC 764266 c.897T>C synonymous_variant 0.17
rpoC 764269 c.900G>C synonymous_variant 0.16
rpoC 764282 c.913_915delTCGinsAGC synonymous_variant 0.17
rpoC 764365 c.996C>T synonymous_variant 0.13
rpoC 764536 c.1167G>C synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.22
rpoC 764560 c.1191T>C synonymous_variant 0.17
rpoC 764566 c.1197C>G synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765658 c.2289C>T synonymous_variant 0.13
rpoC 765700 c.2331T>C synonymous_variant 0.15
rpoC 765734 c.2365T>C synonymous_variant 0.16
rpoC 765739 c.2370G>C synonymous_variant 0.16
rpoC 765753 p.Asp795Ala missense_variant 0.14
rpoC 765796 c.2427C>T synonymous_variant 0.15
rpoC 765814 c.2445A>G synonymous_variant 0.14
rpoC 765835 c.2466C>T synonymous_variant 0.14
rpoC 766726 c.3357T>C synonymous_variant 0.14
rpoC 766738 c.3369G>T synonymous_variant 0.15
rpoC 766750 c.3381C>G synonymous_variant 0.16
rpoC 766765 c.3396A>C synonymous_variant 0.14
rpoC 766774 c.3405T>C synonymous_variant 0.16
rpoC 766804 c.3435A>G synonymous_variant 0.17
rpoC 766843 c.3474T>C synonymous_variant 0.17
rpoC 766861 c.3492G>C synonymous_variant 0.16
rpoC 766864 c.3495G>C synonymous_variant 0.16
rpoC 766894 c.3525T>C synonymous_variant 0.16
rpoC 766895 c.3526T>C synonymous_variant 0.16
rpoC 766900 c.3531T>C synonymous_variant 0.16
rpoC 766933 c.3564A>G synonymous_variant 0.19
rpoC 766945 c.3576A>G synonymous_variant 0.2
rpoC 766963 c.3594T>C synonymous_variant 0.19
rpoC 766972 c.3603G>C synonymous_variant 0.19
rpoC 766978 c.3609C>G synonymous_variant 0.19
rpoC 766996 c.3627C>T synonymous_variant 0.22
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.24
rpoC 767014 c.3645G>C synonymous_variant 0.23
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.2
rpoC 767059 c.3690T>G synonymous_variant 0.17
rpoC 767062 c.3693C>A synonymous_variant 0.16
rpoC 767074 c.3705T>C synonymous_variant 0.15
rpoC 767098 c.3729T>C synonymous_variant 0.14
rpoC 767123 p.Val1252Leu missense_variant 0.91
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781715 c.156T>C synonymous_variant 0.14
rpsL 781841 c.282C>G synonymous_variant 0.14
rpsL 781898 c.339A>T synonymous_variant 0.14
rplC 800771 c.-38C>T upstream_gene_variant 0.14
fbiC 1303584 c.654C>G synonymous_variant 0.14
fbiC 1303590 c.660A>G synonymous_variant 0.14
fbiC 1303854 c.924T>C synonymous_variant 0.14
fbiC 1303860 c.930A>C synonymous_variant 0.16
fbiC 1303881 c.951G>C synonymous_variant 0.21
fbiC 1303884 c.954T>G synonymous_variant 0.21
fbiC 1303911 c.981G>C synonymous_variant 0.18
fbiC 1303914 c.984C>G synonymous_variant 0.17
fbiC 1303920 c.990C>G synonymous_variant 0.17
fbiC 1303923 c.993C>T synonymous_variant 0.16
fbiC 1303929 c.999G>C synonymous_variant 0.16
fbiC 1303947 c.1017T>C synonymous_variant 0.17
fbiC 1303948 p.Gly340Arg missense_variant 0.16
fbiC 1303969 p.Val347Ile missense_variant 0.14
fbiC 1303973 p.Gly348Ala missense_variant 0.15
fbiC 1303981 p.Val351Ile missense_variant 0.17
fbiC 1303995 c.1065C>T synonymous_variant 0.18
fbiC 1304001 c.1071C>G synonymous_variant 0.18
fbiC 1304008 c.1078T>C synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472770 n.925C>A non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.17
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.21
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.2
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.2
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.2
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.67
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.67
rrl 1474962 n.1306delG non_coding_transcript_exon_variant 0.67
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.67
rrl 1474991 n.1334T>C non_coding_transcript_exon_variant 0.67
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.67
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.67
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.14
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.14
fabG1 1673553 p.Asp38Glu missense_variant 0.22
rpsA 1833661 c.120A>G synonymous_variant 0.15
rpsA 1833667 c.126C>G synonymous_variant 0.13
rpsA 1833790 c.249T>A synonymous_variant 0.13
rpsA 1833799 c.258C>G synonymous_variant 0.14
rpsA 1833928 c.387G>C synonymous_variant 0.15
rpsA 1833940 c.399C>G synonymous_variant 0.16
rpsA 1833970 c.429G>C synonymous_variant 0.16
rpsA 1833979 c.438T>C synonymous_variant 0.17
rpsA 1834000 c.459G>C synonymous_variant 0.18
rpsA 1834015 c.474G>C synonymous_variant 0.17
rpsA 1834021 c.480C>T synonymous_variant 0.17
rpsA 1834097 p.Ser186Thr missense_variant 0.13
rpsA 1834189 c.648G>C synonymous_variant 0.14
rpsA 1834195 c.654G>C synonymous_variant 0.17
rpsA 1834201 c.660C>T synonymous_variant 0.18
rpsA 1834222 c.681T>C synonymous_variant 0.21
rpsA 1834225 c.684C>G synonymous_variant 0.21
rpsA 1834240 c.699T>C synonymous_variant 0.19
rpsA 1834249 c.708T>C synonymous_variant 0.17
rpsA 1834261 c.720A>C synonymous_variant 0.16
rpsA 1834264 c.723G>C synonymous_variant 0.17
rpsA 1834297 c.756C>G synonymous_variant 0.19
rpsA 1834303 c.762T>G synonymous_variant 0.19
rpsA 1834306 c.765T>C synonymous_variant 0.17
rpsA 1834348 c.807T>C synonymous_variant 0.14
rpsA 1834366 c.825A>G synonymous_variant 0.14
rpsA 1834375 c.834G>A synonymous_variant 0.15
rpsA 1834396 c.855G>C synonymous_variant 0.17
rpsA 1834411 c.870T>C synonymous_variant 0.16
rpsA 1834417 c.876G>C synonymous_variant 0.15
rpsA 1834423 c.882G>C synonymous_variant 0.15
rpsA 1834465 c.924T>C synonymous_variant 0.14
rpsA 1834468 c.927A>G synonymous_variant 0.15
rpsA 1834474 c.933C>G synonymous_variant 0.14
rpsA 1834498 c.957C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102307 p.Gly246Ser missense_variant 0.99
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518768 c.654C>G synonymous_variant 0.14
pepQ 2860159 p.Ala87Gly missense_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.89
thyA 3073925 c.547T>C synonymous_variant 0.18
thyA 3073929 c.543T>C synonymous_variant 0.18
thyA 3073953 c.519T>C synonymous_variant 0.2
thyA 3073977 c.495A>G synonymous_variant 0.21
thyA 3073989 c.483T>C synonymous_variant 0.19
thyA 3074001 c.471C>G synonymous_variant 0.18
thyA 3074004 c.468T>C synonymous_variant 0.18
thyA 3074010 c.462C>G synonymous_variant 0.18
thyA 3074031 c.441T>C synonymous_variant 0.16
thyA 3074037 c.435C>G synonymous_variant 0.17
thyA 3074076 c.396C>G synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.64
fbiD 3339740 p.Ala208Glu missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3877613 p.Ile299Val missense_variant 0.15
rpoA 3878025 c.483C>T synonymous_variant 0.13
rpoA 3878028 c.480G>C synonymous_variant 0.14
rpoA 3878031 c.477T>C synonymous_variant 0.14
rpoA 3878040 c.468T>C synonymous_variant 0.15
rpoA 3878082 c.426T>C synonymous_variant 0.14
rpoA 3878169 c.339G>C synonymous_variant 0.17
rpoA 3878184 c.324C>T synonymous_variant 0.16
rpoA 3878187 c.321C>G synonymous_variant 0.16
rpoA 3878193 c.315T>C synonymous_variant 0.15
rpoA 3878199 c.309T>C synonymous_variant 0.15
rpoA 3878202 c.306G>C synonymous_variant 0.16
rpoA 3878217 c.291A>G synonymous_variant 0.18
rpoA 3878220 c.288C>T synonymous_variant 0.2
rpoA 3878271 c.237T>C synonymous_variant 0.2
rpoA 3878284 p.Glu75Ala missense_variant 0.2
rpoA 3878292 c.216T>C synonymous_variant 0.2
rpoA 3878298 c.210A>G synonymous_variant 0.21
rpoA 3878304 c.204G>C synonymous_variant 0.2
rpoA 3878313 c.195G>C synonymous_variant 0.19
rpoA 3878322 c.186A>G synonymous_variant 0.17
rpoA 3878331 c.177A>G synonymous_variant 0.17
rpoA 3878334 c.174T>C synonymous_variant 0.17
rpoA 3878337 c.171T>C synonymous_variant 0.18
rpoA 3878346 c.162T>C synonymous_variant 0.2
rpoA 3878364 c.144A>G synonymous_variant 0.17
rpoA 3878367 c.141C>G synonymous_variant 0.17
rpoA 3878370 c.138T>C synonymous_variant 0.16
rpoA 3878376 c.132G>C synonymous_variant 0.17
rpoA 3878385 c.123C>G synonymous_variant 0.16
rpoA 3878391 c.117T>C synonymous_variant 0.16
rpoA 3878396 c.112C>T synonymous_variant 0.17
rpoA 3878436 c.72A>G synonymous_variant 0.15
rpoA 3878442 c.66G>C synonymous_variant 0.15
rpoA 3878454 c.54A>C synonymous_variant 0.15
rpoA 3878472 p.Asp12Glu missense_variant 0.15
rpoA 3878478 c.30C>G synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.89
clpC1 4038740 c.1965G>C synonymous_variant 0.17
clpC1 4038755 c.1950G>C synonymous_variant 0.17
clpC1 4038773 c.1932T>C synonymous_variant 0.17
clpC1 4038782 c.1923G>C synonymous_variant 0.16
clpC1 4038790 c.1915C>T synonymous_variant 0.15
clpC1 4038953 c.1752A>G synonymous_variant 0.15
clpC1 4038974 c.1731T>C synonymous_variant 0.14
clpC1 4038989 c.1716T>C synonymous_variant 0.15
clpC1 4039576 p.Ala377Ser missense_variant 0.15
clpC1 4039577 c.1128T>C synonymous_variant 0.15
clpC1 4039586 c.1119G>C synonymous_variant 0.15
clpC1 4039610 c.1095G>C synonymous_variant 0.15
clpC1 4039616 c.1089G>C synonymous_variant 0.16
clpC1 4039622 c.1083C>G synonymous_variant 0.17
clpC1 4039682 c.1023C>G synonymous_variant 0.14
clpC1 4039724 c.981A>G synonymous_variant 0.15
clpC1 4039748 c.957G>C synonymous_variant 0.16
clpC1 4039991 c.714G>A synonymous_variant 0.89
clpC1 4040354 c.351A>G synonymous_variant 0.15
clpC1 4040369 c.336C>G synonymous_variant 0.14
clpC1 4040380 c.325T>C synonymous_variant 0.14
clpC1 4040387 c.318A>G synonymous_variant 0.16
clpC1 4040393 c.312G>C synonymous_variant 0.16
clpC1 4040411 c.294T>C synonymous_variant 0.16
clpC1 4040423 c.282A>G synonymous_variant 0.16
clpC1 4040426 c.279T>C synonymous_variant 0.16
clpC1 4040431 c.274T>C synonymous_variant 0.15
embC 4240409 p.Pro183Ala missense_variant 0.19
embC 4240819 c.957A>G synonymous_variant 0.17
embC 4240831 c.969T>G synonymous_variant 0.19
embC 4240867 c.1005T>G synonymous_variant 0.16
embC 4240870 c.1008T>C synonymous_variant 0.16
embC 4240879 c.1017G>C synonymous_variant 0.15
embC 4240880 p.Ala340Thr missense_variant 0.15
embC 4240885 c.1023T>C synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247723 p.Pro404Ala missense_variant 0.95
embB 4248097 c.1584C>G synonymous_variant 0.14
embB 4248118 c.1605T>C synonymous_variant 0.15
embB 4248127 c.1614G>C synonymous_variant 0.15
embB 4248133 c.1620C>G synonymous_variant 0.15
embB 4248142 c.1629T>C synonymous_variant 0.14
embB 4248143 c.1630T>C synonymous_variant 0.14
embB 4248157 c.1644A>G synonymous_variant 0.17
embB 4248220 c.1707A>G synonymous_variant 0.15
embB 4248241 c.1728C>T synonymous_variant 0.14
whiB6 4338440 c.81dupT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0