TB-Profiler result

Run: SRR1173800
Summary

Run ID: SRR1173800

Sample name:

Date: 03-04-2023 03:32:02

Number of reads: 916118

Percentage reads mapped: 32.13

Strain: lineage3;lineage2.2

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.74
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.35
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 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.23 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid
katG 2155700 p.Asn138His missense_variant 0.89 isoniazid
pncA 2288883 p.Leu120Pro missense_variant 0.17 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.33 kanamycin
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol
ethA 4326183 c.1290delC frameshift_variant 0.26 ethionamide, ethionamide
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 6304 c.-998C>G upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7930 p.Ala210Asp missense_variant 0.14
gyrA 7964 c.663G>A synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491173 c.391C>A synonymous_variant 0.33
fgd1 491283 c.501C>T synonymous_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.24
rpoB 759746 c.-61C>T upstream_gene_variant 0.63
rpoB 760461 p.Arg219Cys missense_variant 0.29
rpoB 761292 p.Val496Met missense_variant 0.64
rpoC 762434 c.-936T>G upstream_gene_variant 0.8
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763702 c.333C>A synonymous_variant 0.25
rpoC 763882 p.Glu171Asp missense_variant 0.17
rpoC 765064 c.1695C>T synonymous_variant 0.15
rpoC 766252 p.Lys961Asn missense_variant 0.12
rpoC 766361 p.Val998Met missense_variant 0.14
rpoC 766628 p.Arg1087Trp missense_variant 0.13
rpoC 766786 p.Gln1139His missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.3
mmpR5 779395 p.Leu136Met missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800982 p.Ser58Arg missense_variant 0.14
fbiC 1304806 p.Pro626Ser missense_variant 0.18
fbiC 1305276 c.2346G>A synonymous_variant 0.14
Rv1258c 1406660 c.681C>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.6
Rv1258c 1406937 p.Ala135Gly missense_variant 0.17
Rv1258c 1407471 c.-131C>A upstream_gene_variant 0.22
embR 1416302 p.Gly349Val missense_variant 0.12
embR 1417196 p.Gly51Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.13
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.35
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.43
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.55
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.56
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.62
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.57
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.54
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.51
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.45
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.5
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.45
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.5
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.11
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.17
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.27
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.34
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.33
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.32
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.31
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.31
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.31
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.35
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.34
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.17
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.21
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.72
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.63
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.73
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.14
rrs 1472917 n.1072G>A non_coding_transcript_exon_variant 0.14
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.29
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.38
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.56
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.56
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.57
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.58
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.59
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.59
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.6
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.34
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.35
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.36
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.35
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.35
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.35
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.35
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.36
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.37
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.39
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.38
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.38
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.62
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.73
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.73
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.77
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.74
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.79
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.76
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.9
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.87
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.9
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.83
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.83
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.84
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.84
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.81
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.85
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.57
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.37
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.41
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.21
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.14
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.14
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.16
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.17
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.17
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.17
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.14
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15
inhA 1674496 p.Pro99Ser missense_variant 0.12
inhA 1674770 p.Ala190Asp missense_variant 0.12
rpsA 1833880 p.Trp113Cys missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 0.32
rpsA 1834497 p.Gly319Val missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101825 c.1218G>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155189 p.Thr308Ile missense_variant 0.12
katG 2155310 p.Gly268Ser missense_variant 0.25
katG 2155364 p.Glu250* stop_gained 0.2
katG 2155780 p.Gly111Asp missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289287 c.-46C>T upstream_gene_variant 0.15
pncA 2289365 c.-125delC upstream_gene_variant 0.57
pncA 2290142 c.-901G>A upstream_gene_variant 0.13
eis 2715451 c.-119C>A upstream_gene_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 0.71
ahpC 2726117 c.-76T>A upstream_gene_variant 0.61
folC 2746570 c.1029C>T synonymous_variant 0.15
Rv2752c 3065475 c.717C>A synonymous_variant 0.2
Rv2752c 3065558 p.Gly212Arg missense_variant 0.15
Rv2752c 3067167 c.-976C>T upstream_gene_variant 0.18
thyX 3067790 c.156C>G synonymous_variant 0.11
thyA 3073907 p.Ala189Ser missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449272 p.Ala257Thr missense_variant 0.13
Rv3083 3449486 p.Gly328Ala missense_variant 0.1
Rv3083 3449733 c.1230G>T synonymous_variant 0.13
Rv3083 3449867 p.Gly455Val missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474161 p.Gly52Val missense_variant 0.25
fprA 3474223 p.Asp73Tyr missense_variant 0.17
fprA 3474618 p.Gln204His missense_variant 0.12
fprA 3474787 p.Arg261Ser missense_variant 0.21
fprA 3474843 p.Lys279Asn missense_variant 0.12
fprA 3475306 p.Gly434Ser missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 0.17
Rv3236c 3612892 c.225G>A synonymous_variant 0.15
fbiA 3640718 p.Cys59Tyr missense_variant 0.18
fbiB 3642877 p.Lys448Arg missense_variant 0.86
alr 3840319 p.Pro368Ser missense_variant 0.18
alr 3841403 p.Glu6Asp missense_variant 0.35
rpoA 3877700 p.His270Asn missense_variant 0.17
ddn 3987045 p.Arg68Gly missense_variant 0.17
clpC1 4040230 p.Gly159Trp missense_variant 0.25
clpC1 4040734 c.-30C>A upstream_gene_variant 0.18
embC 4240774 c.912C>A synonymous_variant 0.18
embC 4240994 p.Ala378Thr missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 0.77
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244649 p.Asp473Tyr missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.12
embB 4247060 p.Pro183Thr missense_variant 0.17
embB 4248327 p.Ala605Val missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.17
ethA 4327519 c.-46C>T upstream_gene_variant 0.18
ethA 4327968 c.-495C>T upstream_gene_variant 0.17
whiB6 4338563 c.-42G>T upstream_gene_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0