TB-Profiler result

Run: SRR1013570
Summary

Run ID: SRR1013570

Sample name:

Date: 02-04-2023 15:55:43

Number of reads: 1188008

Percentage reads mapped: 20.4

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.89 isoniazid, ethionamide
katG 2155693 p.Ser140Asn missense_variant 0.48 isoniazid
katG 2155732 p.Gln127Pro missense_variant 0.47 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.88 pyrazinamide
folC 2747151 p.Ser150Gly missense_variant 0.9 para-aminosalicylic_acid
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4326459 c.1004_1014delCTGACATCATC frameshift_variant 0.88 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.9
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762872 p.Met1022Ile missense_variant 0.17
rpoB 762878 p.Ile1024Met missense_variant 0.17
rpoB 762879 p.Met1025Leu missense_variant 0.17
rpoC 762893 c.-477C>T upstream_gene_variant 0.37
rpoC 762896 c.-474G>C upstream_gene_variant 0.38
rpoC 762917 c.-453C>G upstream_gene_variant 0.43
rpoC 762920 c.-450C>T upstream_gene_variant 0.42
rpoC 762923 c.-447C>G upstream_gene_variant 0.43
rpoB 762925 p.Thr1040Ile missense_variant 0.42
rpoC 762929 c.-441G>T upstream_gene_variant 0.42
rpoB 762939 p.Met1045Leu missense_variant 0.39
rpoB 762942 p.Ile1046Val missense_variant 0.39
rpoC 762965 c.-405T>C upstream_gene_variant 0.38
rpoC 762980 c.-390T>C upstream_gene_variant 0.28
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 762995 c.-375G>C upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764338 p.Glu323Asp missense_variant 0.17
rpoC 764344 c.975C>T synonymous_variant 0.29
rpoC 764348 p.Met327Leu missense_variant 0.3
rpoC 764355 p.Gln329Pro missense_variant 0.3
rpoC 764377 c.1008C>G synonymous_variant 0.32
rpoC 764380 c.1011G>C synonymous_variant 0.35
rpoC 764383 c.1014C>G synonymous_variant 0.36
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.35
rpoC 764398 c.1029G>C synonymous_variant 0.33
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.32
rpoC 764410 c.1041G>T synonymous_variant 0.36
rpoC 764428 c.1059G>T synonymous_variant 0.24
rpoC 764587 c.1218C>G synonymous_variant 0.11
rpoC 764593 c.1224C>T synonymous_variant 0.16
rpoC 764611 c.1242G>C synonymous_variant 0.17
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764641 c.1272C>T synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764656 c.1287C>G synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.91
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.28
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.32
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.44
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.43
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.47
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.45
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.39
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.37
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.35
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.31
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.31
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.24
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.1
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.17
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.19
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.5
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.45
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.3
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.25
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.25
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.32
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.34
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.38
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.38
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.37
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.36
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.37
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.36
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.38
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.38
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.4
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.86
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.14
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.15
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.13
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.14
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.14
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.15
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.16
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.2
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.19
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.19
rrl 1475894 n.2237C>A non_coding_transcript_exon_variant 0.2
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.36
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.45
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.45
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.46
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.45
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.47
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.6
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.64
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.54
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.47
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.47
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.44
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.42
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.24
rpsA 1833594 p.Ser18Tyr missense_variant 0.94
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101763 p.Gly427Val missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155617 p.Ile165Met missense_variant 0.12
katG 2155626 c.486G>C synonymous_variant 0.26
katG 2155637 p.Leu159Ile missense_variant 0.32
katG 2155641 p.Lys157Arg missense_variant 0.33
katG 2155650 c.462G>A synonymous_variant 0.3
katG 2155655 p.Lys153Gln missense_variant 0.33
katG 2155661 p.Val151Ile missense_variant 0.35
katG 2155668 c.444G>C synonymous_variant 0.42
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.48
katG 2155704 c.408C>T synonymous_variant 0.61
katG 2155716 c.396T>C synonymous_variant 0.55
katG 2155722 c.390G>C synonymous_variant 0.5
katG 2155728 c.384G>C synonymous_variant 0.47
katG 2155735 p.Met126Gln missense_variant 0.47
katG 2155737 c.375C>T synonymous_variant 0.5
katG 2155741 p.Gly124Ala missense_variant 0.5
katG 2155743 c.369G>T synonymous_variant 0.47
katG 2155765 p.His116Thr missense_variant 0.44
katG 2155782 c.330C>G synonymous_variant 0.29
katG 2155785 p.Ala109Ser missense_variant 0.29
katG 2155794 c.318G>C synonymous_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725931 c.-262_-261insGG upstream_gene_variant 0.14
ahpC 2726146 c.-47_-46insT upstream_gene_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448958 p.Asp152Ala missense_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474765 c.759T>C synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841405 p.Glu6Gln missense_variant 0.92
rpoA 3877960 p.Val183Gly missense_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244984 p.Leu584Phe missense_variant 0.13
aftB 4267647 p.Asp397Gly 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