TB-Profiler result

Run: SRR1173799
Summary

Run ID: SRR1173799

Sample name:

Date: 03-04-2023 03:31:58

Number of reads: 677422

Percentage reads mapped: 38.18

Strain: lineage3.1.1

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 0.68
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.71
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.65
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
rpoB 761155 p.Ser450Leu missense_variant 0.4 rifampicin
katG 2154841 p.Ala424Glu missense_variant 0.12 isoniazid
katG 2155826 c.281_285delACTAC frameshift_variant 0.2 isoniazid
katG 2155836 c.275_276insGTAGT frameshift_variant&stop_gained 0.22 isoniazid
katG 2155843 p.Trp90* stop_gained 0.25 isoniazid
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
gyrB 5742 p.Gly168Val missense_variant 0.17
gyrB 6362 p.Leu375Met missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.408G>A synonymous_variant 0.36
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490934 p.Ala51Val missense_variant 0.12
fgd1 491602 p.Ala274Thr missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.65
mshA 575616 p.Thr90Ile missense_variant 0.2
mshA 575663 p.Gly106Trp missense_variant 0.13
ccsA 619763 c.-128C>A upstream_gene_variant 0.15
ccsA 620374 p.Pro162Thr missense_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.46
rpoB 760088 c.282C>A synonymous_variant 0.13
rpoB 761575 p.Phe590Tyr missense_variant 0.12
rpoB 761579 c.1773G>C synonymous_variant 0.13
rpoB 761600 c.1794T>C synonymous_variant 0.15
rpoB 761612 c.1806G>T synonymous_variant 0.18
rpoB 761615 c.1809A>G synonymous_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 0.75
rpoB 762780 p.Gly992Cys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764620 c.1251G>A synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 0.29
rpoC 766488 p.Pro1040Arg missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.6
mmpL5 777200 c.1281C>G synonymous_variant 0.13
mmpL5 777821 c.660G>A synonymous_variant 0.15
mmpS5 778849 c.55_56delGC frameshift_variant 0.12
mmpL5 778915 c.-435G>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781433 c.-127C>A upstream_gene_variant 0.17
rplC 801115 p.Ala103Ser missense_variant 0.14
Rv1258c 1406174 c.1167C>T synonymous_variant 0.2
embR 1416795 p.Gly185Trp missense_variant 0.14
embR 1417122 p.Val76Leu missense_variant 0.14
embR 1417241 p.Arg36Leu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.17
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.24
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.24
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.26
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.26
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.26
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.25
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.25
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.38
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.2
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.18
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.19
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.61
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.29
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.14
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.21
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.5
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.64
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.48
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.29
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.5
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.38
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.48
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.12
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.1
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 0.16
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.19
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.11
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.14
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.15
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.21
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.14
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.14
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.51
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.59
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.59
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.15
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.1
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.13
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.12
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.3
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.34
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.31
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.11
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.37
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.24
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.21
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.11
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.12
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.16
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.13
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.41
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.37
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.35
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.34
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.32
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.33
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.33
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.31
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.31
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.32
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.32
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.33
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.2
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.21
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.18
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.2
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.22
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.39
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.47
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.41
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.53
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.38
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.56
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.4
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.48
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.66
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.55
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.51
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.54
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.39
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.55
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.43
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.56
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.61
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.16
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.1
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.2
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.17
rpsA 1834850 p.Ala437Ser missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102334 p.Gln237Lys missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 0.47
katG 2155820 p.Tyr98His missense_variant 0.17
katG 2155834 p.Ala93Gly missense_variant 0.2
katG 2156030 p.Tyr28Asn missense_variant 0.17
katG 2156050 p.Pro21His missense_variant 0.15
katG 2156262 c.-151C>A upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.65
PPE35 2168014 p.Ala867Thr missense_variant 0.12
PPE35 2168982 p.Thr544Ile missense_variant 0.12
PPE35 2169068 c.1545G>C synonymous_variant 0.11
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2170461 p.Gly51Glu missense_variant 0.6
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.86
pncA 2289365 c.-125delC upstream_gene_variant 0.79
pncA 2289452 c.-211C>A upstream_gene_variant 0.14
pncA 2290108 c.-867C>A upstream_gene_variant 0.15
ahpC 2725956 c.-237G>T upstream_gene_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 0.79
folC 2746180 c.1419C>T synonymous_variant 0.15
Rv2752c 3066225 c.-34G>A upstream_gene_variant 0.17
thyX 3067675 p.His91Asn missense_variant 0.13
thyA 3073808 p.Arg222Ser missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.67
Rv3083 3448369 c.-135G>A upstream_gene_variant 0.12
fprA 3473870 c.-137C>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474177 c.171C>T synonymous_variant 0.46
whiB7 3568473 p.Glu69Asp missense_variant 0.15
alr 3841086 p.Trp112Leu missense_variant 0.12
ddn 3986906 p.Met21Ile missense_variant 0.12
ddn 3987199 p.Arg119Leu missense_variant 0.18
clpC1 4040824 c.-120C>A upstream_gene_variant 0.15
embC 4240172 p.Val104Met missense_variant 0.44
embC 4241562 p.Arg567His missense_variant 0.65
embC 4242075 p.Arg738Gln missense_variant 0.68
embA 4242505 c.-728G>T upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245962 c.-552G>A upstream_gene_variant 0.33
aftB 4268496 p.Arg114Gln missense_variant 0.18
ubiA 4269670 p.Val55Gly missense_variant 0.56
ethA 4326432 p.Leu348Ile missense_variant 0.13
ethA 4326454 c.1020C>T synonymous_variant 0.22
ethR 4326778 c.-771G>T upstream_gene_variant 0.18
ethA 4327863 c.-390G>A upstream_gene_variant 0.13
ethA 4328329 c.-856C>G upstream_gene_variant 0.13
whiB6 4338187 p.Ser112Tyr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.36
gid 4407742 p.Arg154Gln missense_variant 0.29