TB-Profiler result

Run: SRR7796666
Summary

Run ID: SRR7796666

Sample name:

Date: 04-04-2023 20:20:48

Number of reads: 378536

Percentage reads mapped: 74.37

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155109 p.Ile335Val missense_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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 6727 c.-575G>T upstream_gene_variant 0.19
gyrA 6730 c.-572A>G upstream_gene_variant 0.19
gyrA 6745 c.-557T>G upstream_gene_variant 0.19
gyrA 6760 c.-542G>C upstream_gene_variant 0.19
gyrA 6778 c.-524C>T upstream_gene_variant 0.19
gyrA 6793 c.-509T>C upstream_gene_variant 0.19
gyrB 6797 p.Gly520Thr missense_variant 0.19
gyrA 6824 c.-478C>T upstream_gene_variant 0.17
gyrA 6841 c.-461T>C upstream_gene_variant 0.16
gyrA 6844 c.-458T>G upstream_gene_variant 0.16
gyrA 6853 c.-449A>G upstream_gene_variant 0.17
gyrA 6856 c.-446T>C upstream_gene_variant 0.17
gyrA 6859 c.-443T>C upstream_gene_variant 0.17
gyrA 6862 c.-440C>G upstream_gene_variant 0.16
gyrA 6878 c.-424T>C upstream_gene_variant 0.16
gyrA 6881 c.-421T>C upstream_gene_variant 0.17
gyrA 6904 c.-398C>G upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7979 c.678G>C synonymous_variant 0.15
gyrA 7992 p.Ala231Ser missense_variant 0.17
gyrA 7997 c.696A>C synonymous_variant 0.17
gyrA 8009 c.708A>C synonymous_variant 0.17
gyrA 8010 p.Ser237Thr missense_variant 0.17
gyrA 8020 p.Thr240Ile missense_variant 0.21
gyrA 8024 c.723T>C synonymous_variant 0.21
gyrA 8027 c.726T>C synonymous_variant 0.21
gyrA 8036 c.735A>G synonymous_variant 0.21
gyrA 8039 c.738T>C synonymous_variant 0.21
gyrA 8054 c.753T>C synonymous_variant 0.27
gyrA 8057 c.756A>G synonymous_variant 0.27
gyrA 8069 c.768T>C synonymous_variant 0.27
gyrA 8078 c.777A>G synonymous_variant 0.27
gyrA 8090 c.789C>G synonymous_variant 0.27
gyrA 8096 c.795T>C synonymous_variant 0.25
gyrA 8099 c.798T>C synonymous_variant 0.25
gyrA 8111 c.810G>C synonymous_variant 0.25
gyrA 8156 c.855T>C synonymous_variant 0.23
gyrA 8168 c.867A>G synonymous_variant 0.21
gyrA 8174 c.873C>G synonymous_variant 0.21
gyrA 8177 c.876A>C synonymous_variant 0.21
gyrA 8198 c.897T>C synonymous_variant 0.24
gyrA 8207 c.906T>C synonymous_variant 0.24
gyrA 8219 c.918T>C synonymous_variant 0.24
gyrA 8225 c.924T>C synonymous_variant 0.24
gyrA 8234 c.933T>G synonymous_variant 0.19
gyrA 8235 c.934_936delTTAinsCTG synonymous_variant 0.19
gyrA 8253 p.Ile318Leu missense_variant 0.19
gyrA 8264 c.963T>C synonymous_variant 0.19
gyrA 8267 c.966G>C synonymous_variant 0.19
gyrA 8270 c.969G>C synonymous_variant 0.19
gyrA 8283 p.Ile328Leu missense_variant 0.17
gyrA 8288 c.987T>C synonymous_variant 0.14
gyrA 8294 c.993T>C synonymous_variant 0.14
gyrA 8619 c.1318T>C synonymous_variant 0.13
gyrA 8624 c.1323G>C synonymous_variant 0.13
gyrA 8627 c.1326C>G synonymous_variant 0.13
gyrA 8642 c.1341A>G synonymous_variant 0.2
gyrA 8645 c.1344C>G synonymous_variant 0.2
gyrA 8672 c.1371A>G synonymous_variant 0.27
gyrA 8693 c.1392T>C synonymous_variant 0.22
gyrA 8699 c.1398A>G synonymous_variant 0.18
gyrA 8711 c.1410A>C synonymous_variant 0.18
gyrA 8714 c.1413A>G synonymous_variant 0.18
gyrA 8717 c.1416C>G synonymous_variant 0.18
gyrA 8720 c.1419G>A synonymous_variant 0.18
gyrA 8729 c.1428T>C synonymous_variant 0.18
gyrA 8732 c.1431G>C synonymous_variant 0.18
gyrA 8747 c.1446A>G synonymous_variant 0.12
gyrA 8756 c.1455A>G synonymous_variant 0.12
gyrA 8762 c.1461G>C synonymous_variant 0.13
gyrA 8765 p.Asp488Glu missense_variant 0.13
gyrA 8767 p.Arg489Lys missense_variant 0.13
gyrA 8779 p.Asp493Ala missense_variant 0.15
gyrA 8786 c.1485T>C synonymous_variant 0.17
gyrA 8796 p.Ile499Val missense_variant 0.17
gyrA 8801 c.1500G>C synonymous_variant 0.17
gyrA 8810 c.1509A>C synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760253 c.447T>C synonymous_variant 0.13
rpoB 760283 c.477G>C synonymous_variant 0.2
rpoB 760307 c.501T>C synonymous_variant 0.14
rpoB 760328 c.522G>C synonymous_variant 0.14
rpoB 760331 c.525G>C synonymous_variant 0.14
rpoB 760337 c.531C>G synonymous_variant 0.13
rpoB 760340 c.534G>C synonymous_variant 0.13
rpoB 760361 c.555T>C synonymous_variant 0.12
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 0.17
rpoB 760522 p.Ser239Asn missense_variant 0.14
rpoB 760532 c.726T>C synonymous_variant 0.14
rpoB 760533 p.Val243Thr missense_variant 0.14
rpoB 760547 c.741G>C synonymous_variant 0.14
rpoB 760661 c.855A>C synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763212 p.Gly1136Cys missense_variant 0.18
rpoC 765553 c.2184C>T synonymous_variant 0.15
rpoC 765556 c.2187G>C synonymous_variant 0.15
rpoC 765559 c.2190G>C synonymous_variant 0.17
rpoC 765578 c.2209C>T synonymous_variant 0.24
rpoC 765583 c.2214G>T synonymous_variant 0.19
rpoC 765613 p.His748Gln missense_variant 0.2
rpoC 765625 c.2256C>G synonymous_variant 0.2
rpoC 765628 c.2259G>C synonymous_variant 0.19
rpoC 765631 p.Asp754Glu missense_variant 0.19
rpoC 765658 c.2289C>T synonymous_variant 0.18
rpoC 765700 c.2331T>C synonymous_variant 0.13
rpoC 765734 c.2365T>C synonymous_variant 0.14
rpoC 765739 c.2370G>C synonymous_variant 0.14
rpoC 765751 c.2382C>G synonymous_variant 0.17
rpoC 765753 p.Asp795Ala missense_variant 0.14
rpoC 765772 c.2403C>G synonymous_variant 0.15
rpoC 765784 c.2415C>G synonymous_variant 0.17
rpoC 765796 c.2427C>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778393 p.Thr30Ala missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302917 c.-14_-13insA upstream_gene_variant 1.0
fbiC 1304520 c.1590A>C synonymous_variant 0.12
fbiC 1304523 c.1593G>T synonymous_variant 0.12
fbiC 1304526 c.1596T>G synonymous_variant 0.12
fbiC 1304544 c.1614T>C synonymous_variant 0.12
fbiC 1304546 p.Val539Ala missense_variant 0.12
fbiC 1304559 p.Glu543Asp missense_variant 0.14
fbiC 1304565 c.1635C>G synonymous_variant 0.14
fbiC 1304568 c.1638T>C synonymous_variant 0.14
fbiC 1304574 c.1644C>G synonymous_variant 0.14
fbiC 1304580 c.1650T>C synonymous_variant 0.14
fbiC 1304613 c.1683T>C synonymous_variant 0.14
fbiC 1304628 c.1698G>C synonymous_variant 0.14
fbiC 1304634 c.1704C>G synonymous_variant 0.14
fbiC 1304640 c.1710A>C synonymous_variant 0.16
fbiC 1304646 c.1716T>C synonymous_variant 0.16
fbiC 1304658 c.1728C>G synonymous_variant 0.18
fbiC 1304670 c.1740G>T synonymous_variant 0.18
fbiC 1304671 p.Val581Thr missense_variant 0.18
fbiC 1304675 p.Gly582Glu missense_variant 0.18
fbiC 1304691 c.1761G>C synonymous_variant 0.17
fbiC 1304694 c.1764A>C synonymous_variant 0.17
fbiC 1304703 c.1773C>G synonymous_variant 0.22
fbiC 1304715 c.1785G>C synonymous_variant 0.2
fbiC 1304724 c.1794A>G synonymous_variant 0.14
fbiC 1304727 c.1797A>G synonymous_variant 0.14
fbiC 1304742 c.1812T>C synonymous_variant 0.17
fbiC 1304748 c.1818T>C synonymous_variant 0.16
fbiC 1304754 c.1824G>A synonymous_variant 0.16
fbiC 1304757 c.1827A>G synonymous_variant 0.17
fbiC 1304991 c.2061G>C synonymous_variant 0.13
fbiC 1304994 c.2064A>G synonymous_variant 0.14
fbiC 1304995 c.2065T>C synonymous_variant 0.14
fbiC 1305006 c.2076A>G synonymous_variant 0.17
fbiC 1305012 c.2082G>C synonymous_variant 0.17
fbiC 1305015 c.2085G>C synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417061 p.Ala96Glu missense_variant 0.13
embR 1417207 c.141C>T synonymous_variant 0.12
embR 1417508 c.-161C>A upstream_gene_variant 0.18
atpE 1460856 c.-189C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471781 n.-65G>T upstream_gene_variant 0.18
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.18
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.18
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.18
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.18
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.17
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.17
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.17
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2
fabG1 1673209 c.-230delT upstream_gene_variant 0.14
fabG1 1673577 p.His46Gln missense_variant 0.22
inhA 1673808 c.-394A>G upstream_gene_variant 0.13
rpsA 1834097 c.556_557delTCinsAG synonymous_variant 0.17
rpsA 1834102 c.561T>C synonymous_variant 0.17
rpsA 1834150 c.609G>C synonymous_variant 0.17
rpsA 1834153 c.612T>C synonymous_variant 0.17
rpsA 1834154 p.Asn205Gln missense_variant 0.17
rpsA 1834157 c.616T>C synonymous_variant 0.2
rpsA 1834162 c.621A>G synonymous_variant 0.2
rpsA 1834165 c.624A>G synonymous_variant 0.17
rpsA 1834169 p.Thr210Ala missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834186 c.645C>G synonymous_variant 0.15
rpsA 1834189 c.648G>C synonymous_variant 0.15
rpsA 1834195 c.654G>C synonymous_variant 0.15
rpsA 1834222 c.681T>C synonymous_variant 0.12
rpsA 1834231 c.690T>C synonymous_variant 0.12
rpsA 1834240 c.699T>C synonymous_variant 0.14
rpsA 1834249 c.708T>C synonymous_variant 0.14
rpsA 1834261 c.720A>C synonymous_variant 0.16
rpsA 1834264 c.723G>C synonymous_variant 0.16
rpsA 1834776 p.Ala412Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154252 p.Ser620Arg missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221795 p.Ile457Asn missense_variant 0.12
Rv1979c 2222899 p.Arg89Gln missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518540 c.426T>G synonymous_variant 0.2
kasA 2518561 c.447T>C synonymous_variant 0.18
kasA 2518567 c.453G>C synonymous_variant 0.18
kasA 2518570 c.456G>C synonymous_variant 0.18
kasA 2518574 p.Ile154Val missense_variant 0.2
kasA 2518588 c.474T>C synonymous_variant 0.25
kasA 2518591 c.477G>C synonymous_variant 0.25
kasA 2518609 p.Met165Ile missense_variant 0.2
kasA 2518621 c.507G>A synonymous_variant 0.15
kasA 2518642 c.528A>G synonymous_variant 0.17
kasA 2518663 c.549T>C synonymous_variant 0.14
kasA 2518672 c.558G>C synonymous_variant 0.12
kasA 2518687 c.573C>T synonymous_variant 0.17
kasA 2518696 c.582C>G synonymous_variant 0.15
kasA 2518702 c.588C>T synonymous_variant 0.15
kasA 2518711 c.597A>G synonymous_variant 0.14
kasA 2518714 c.600A>C synonymous_variant 0.14
kasA 2518732 c.618C>G synonymous_variant 0.13
eis 2714888 p.Phe149Leu missense_variant 0.17
pepQ 2860513 c.-95A>G upstream_gene_variant 0.15
Rv2752c 3065538 c.654G>T synonymous_variant 0.18
Rv2752c 3065883 c.309C>T synonymous_variant 0.14
thyX 3067948 c.-3G>A upstream_gene_variant 1.0
thyA 3073924 c.534_547delCGCCAGCTATGCGT frameshift_variant 1.0
thyA 3074100 c.372T>C synonymous_variant 0.15
thyA 3074128 p.Ala115Val missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449864 p.Gln454Leu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
rpoA 3878698 c.-191A>G upstream_gene_variant 0.33
rpoA 3878701 c.-194C>G upstream_gene_variant 0.33
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039524 p.Phe394Tyr missense_variant 0.14
clpC1 4039526 c.1179G>C synonymous_variant 0.14
clpC1 4039547 c.1158C>G synonymous_variant 0.2
clpC1 4039553 c.1152C>G synonymous_variant 0.2
clpC1 4039562 c.1143C>G synonymous_variant 0.2
clpC1 4039565 c.1140G>C synonymous_variant 0.14
clpC1 4039576 p.Ala377Ser missense_variant 0.15
clpC1 4039577 c.1128T>C synonymous_variant 0.15
clpC1 4039586 c.1119G>C synonymous_variant 0.16
clpC1 4039610 c.1095G>C synonymous_variant 0.17
clpC1 4039616 c.1089G>C synonymous_variant 0.18
clpC1 4039622 c.1083C>G synonymous_variant 0.18
clpC1 4039682 c.1023C>G synonymous_variant 0.2
clpC1 4039685 c.1020C>T synonymous_variant 0.2
clpC1 4039724 c.981A>G synonymous_variant 0.17
clpC1 4039736 c.969C>A synonymous_variant 0.12
clpC1 4039748 c.957G>C synonymous_variant 0.17
clpC1 4039751 c.954A>G synonymous_variant 0.17
clpC1 4039757 c.948A>G synonymous_variant 0.13
clpC1 4039760 c.945T>C synonymous_variant 0.13
clpC1 4039769 c.936C>G synonymous_variant 0.14
clpC1 4039778 c.927A>G synonymous_variant 0.13
clpC1 4039781 c.924G>C synonymous_variant 0.13
clpC1 4039787 c.916_918delTCGinsAGC synonymous_variant 0.13
clpC1 4039793 c.912C>G synonymous_variant 0.13
clpC1 4039817 c.888A>T synonymous_variant 0.15
clpC1 4039820 c.885T>G synonymous_variant 0.15
clpC1 4039831 c.874T>C synonymous_variant 0.12
clpC1 4039832 c.873C>G synonymous_variant 0.12
clpC1 4039850 c.855T>C synonymous_variant 0.12
clpC1 4039865 c.840T>C synonymous_variant 0.12
clpC1 4040225 c.480A>C synonymous_variant 0.12
clpC1 4040228 c.477G>C synonymous_variant 0.12
clpC1 4040234 c.471C>G synonymous_variant 0.12
clpC1 4040237 c.468C>T synonymous_variant 0.12
clpC1 4040249 c.456A>G synonymous_variant 0.14
clpC1 4040457 c.247delC frameshift_variant 0.15
embC 4240819 c.957A>G synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243598 c.366G>A synonymous_variant 1.0
embB 4246286 c.-228G>C upstream_gene_variant 0.12
embB 4247419 c.906C>T synonymous_variant 0.12
embB 4247872 c.1359C>T synonymous_variant 0.96
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 1.0
whiB6 4338326 p.Ala66Thr missense_variant 1.0
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