TB-Profiler result

Run: SRR12882155
Summary

Run ID: SRR12882155

Sample name:

Date: 03-04-2023 07:13:47

Number of reads: 898465

Percentage reads mapped: 97.0

Strain: lineage1.2.2.2

Drug-resistance: RR-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
lineage1 Indo-Oceanic EAI RD239 0.98
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 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
rpoB 761122 p.Pro439Leu missense_variant 0.17 rifampicin
rpsA 1834962 p.Arg474Leu missense_variant 0.18 pyrazinamide
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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 5630 c.391C>T synonymous_variant 1.0
gyrB 5878 c.639G>T synonymous_variant 0.17
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8141 c.840C>T synonymous_variant 0.15
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491075 p.Pro98Gln missense_variant 0.17
fgd1 491144 p.Ala121Asp missense_variant 0.17
fgd1 491170 p.Ala130Ser missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575482 c.135C>A synonymous_variant 0.17
mshA 576104 p.Arg253Ser missense_variant 0.18
mshA 576111 p.Ala255Asp missense_variant 0.2
mshA 576186 p.Pro280His missense_variant 0.18
mshA 576241 c.894C>A synonymous_variant 0.17
mshA 576290 p.Leu315Ile missense_variant 0.15
ccsA 619699 c.-192G>T upstream_gene_variant 0.2
ccsA 619805 c.-86C>T upstream_gene_variant 0.17
ccsA 620016 c.126C>A synonymous_variant 0.15
ccsA 620424 c.534G>T synonymous_variant 0.22
ccsA 620782 p.Ala298Ser missense_variant 0.18
ccsA 620864 c.974G>T stop_lost&splice_region_variant 0.2
rpoB 760109 p.Phe101Leu missense_variant 0.4
rpoB 760864 p.Gly353Val missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763058 c.-312C>A upstream_gene_variant 0.15
rpoC 763711 c.342G>T synonymous_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764593 c.1224C>A synonymous_variant 0.18
rpoC 764939 p.Leu524Met missense_variant 0.17
rpoC 765358 p.Met663Ile missense_variant 0.5
rpoC 765484 c.2115G>A synonymous_variant 0.4
rpoC 765500 p.Gln711Lys missense_variant 0.4
rpoC 765541 c.2172C>A synonymous_variant 0.29
rpoC 766917 p.Arg1183His missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775682 c.2799C>A synonymous_variant 0.22
mmpL5 775751 c.2730C>T synonymous_variant 0.2
mmpL5 776030 c.2451G>T synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776260 p.Ala741Thr missense_variant 0.15
mmpL5 776789 c.1692C>A synonymous_variant 0.25
mmpL5 777174 p.Arg436His missense_variant 0.17
mmpL5 777185 c.1296G>T synonymous_variant 0.17
mmpL5 777702 p.Thr260Asn missense_variant 0.17
mmpL5 778201 p.Val94Met missense_variant 0.17
mmpL5 779118 c.-638C>T upstream_gene_variant 0.4
mmpL5 779361 c.-881C>T upstream_gene_variant 0.25
mmpL5 779397 c.-917C>T upstream_gene_variant 0.25
mmpS5 779506 c.-601C>A upstream_gene_variant 0.22
mmpS5 779510 c.-605C>A upstream_gene_variant 0.22
rpsL 781382 c.-178T>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781556 c.-4G>T upstream_gene_variant 0.18
rpsL 781667 c.108C>A synonymous_variant 0.2
rplC 800669 c.-140G>T upstream_gene_variant 0.23
rplC 800853 p.Gln15His missense_variant 0.11
rplC 801235 p.Ala143Ser missense_variant 0.15
fbiC 1303701 c.771C>T synonymous_variant 0.18
fbiC 1303705 p.Leu259Met missense_variant 0.17
fbiC 1304449 p.Ala507Thr missense_variant 0.33
fbiC 1304911 p.Leu661Met missense_variant 0.29
fbiC 1304924 p.Pro665Gln missense_variant 0.25
Rv1258c 1406710 p.Gly211Arg missense_variant 0.25
Rv1258c 1406954 c.387C>A synonymous_variant 0.17
embR 1416952 c.396A>G synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417343 p.Ala2Asp missense_variant 0.17
embR 1417456 c.-109G>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471720 n.-126G>T upstream_gene_variant 0.18
rrs 1471793 n.-53G>A upstream_gene_variant 0.15
rrs 1472019 n.174G>T non_coding_transcript_exon_variant 0.25
rrs 1472920 n.1075G>T non_coding_transcript_exon_variant 0.13
rrl 1473605 n.-53G>A upstream_gene_variant 0.2
rrl 1474307 n.650G>A non_coding_transcript_exon_variant 0.14
rrl 1474409 n.752G>T non_coding_transcript_exon_variant 0.17
rrl 1474701 n.1044C>A non_coding_transcript_exon_variant 0.2
rrl 1474948 n.1291C>A non_coding_transcript_exon_variant 0.33
rrl 1475186 n.1529C>T non_coding_transcript_exon_variant 0.25
rrl 1475397 n.1740G>T non_coding_transcript_exon_variant 0.18
rrl 1475523 n.1866G>T non_coding_transcript_exon_variant 0.15
rrl 1475726 n.2069G>T non_coding_transcript_exon_variant 0.2
rrl 1475749 n.2092G>T non_coding_transcript_exon_variant 0.18
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14
fabG1 1673437 c.-3G>T upstream_gene_variant 0.2
inhA 1674255 p.Asp18Glu missense_variant 0.22
inhA 1674424 p.Ala75Ser missense_variant 0.25
inhA 1674474 c.273G>A synonymous_variant 0.18
inhA 1674495 p.Met98Ile missense_variant 0.18
rpsA 1833478 c.-64G>T upstream_gene_variant 0.22
rpsA 1834402 c.861C>T synonymous_variant 0.5
rpsA 1834478 p.Val313Phe missense_variant 0.2
rpsA 1834512 p.Ser324Tyr missense_variant 0.18
rpsA 1834684 c.1143C>A synonymous_variant 0.18
tlyA 1917758 c.-182G>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101870 c.1173C>T synonymous_variant 0.18
ndh 2101961 p.Pro361Gln missense_variant 0.22
ndh 2102240 p.Arg268His missense_variant 1.0
ndh 2102422 c.621C>A synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154941 p.Glu391* stop_gained 0.2
katG 2154971 p.Asp381Tyr missense_variant 0.22
katG 2154987 c.1125G>T synonymous_variant 0.25
katG 2155018 p.Pro365Gln missense_variant 0.22
katG 2155029 c.1083C>A synonymous_variant 0.22
katG 2155223 p.Gly297Cys missense_variant 0.29
katG 2155757 p.Arg119Ser missense_variant 0.18
katG 2155993 p.Pro40His missense_variant 0.22
katG 2156042 p.Gly24Cys missense_variant 0.22
PPE35 2167857 p.Trp919Leu missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169023 c.1590G>T synonymous_variant 0.4
PPE35 2169668 c.945C>A synonymous_variant 0.17
PPE35 2170013 c.600C>A synonymous_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.3
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2221975 p.Ala397Glu missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223026 p.Ala47Ser missense_variant 0.18
Rv1979c 2223045 c.120C>A synonymous_variant 0.18
Rv1979c 2223145 p.Arg7Ile missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288861 p.Glu127Asp missense_variant 0.15
pncA 2289500 c.-260delG upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518757 p.Ala215Thr missense_variant 0.25
kasA 2518769 p.Arg219Ser missense_variant 0.22
kasA 2519355 p.Gly414Glu missense_variant 0.17
eis 2714149 p.Pro395Arg missense_variant 0.11
ahpC 2726029 c.-164G>C upstream_gene_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726088 c.-105G>A upstream_gene_variant 0.2
ahpC 2726377 p.Pro62His missense_variant 0.25
ahpC 2726442 p.Gly84Trp missense_variant 0.18
ahpC 2726659 p.Arg156Leu missense_variant 0.15
pepQ 2859547 p.Gly291Asp missense_variant 0.22
pepQ 2859586 p.Arg278Leu missense_variant 0.17
ribD 2986979 c.141C>T synonymous_variant 0.25
ribD 2987261 p.Leu141Phe missense_variant 0.21
Rv2752c 3064810 p.Thr461Ile missense_variant 0.2
Rv2752c 3065020 p.Arg391His missense_variant 0.18
Rv2752c 3065389 p.Arg268His missense_variant 0.29
Rv2752c 3065519 p.Leu225Ile missense_variant 0.14
Rv2752c 3065790 c.402C>A synonymous_variant 0.18
thyX 3067346 c.600C>A synonymous_variant 0.22
thyX 3067773 p.Ala58Val missense_variant 0.22
thyA 3073687 p.Ala262Val missense_variant 0.22
thyA 3073937 p.Ala179Thr missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087601 p.Gly261Val missense_variant 1.0
fbiD 3339288 c.171C>A synonymous_variant 0.18
fbiD 3339434 p.Gly106Val missense_variant 0.18
fbiD 3339438 c.321C>T synonymous_variant 0.18
Rv3083 3448707 c.204G>A synonymous_variant 0.18
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449286 p.Trp261Cys missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474027 c.21C>T synonymous_variant 0.29
fprA 3474089 p.Thr28Met missense_variant 0.17
fprA 3474282 p.Glu92Asp missense_variant 0.14
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475071 c.1065C>T synonymous_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568691 c.-12G>T upstream_gene_variant 0.13
whiB7 3568702 c.-23C>T upstream_gene_variant 0.15
Rv3236c 3612034 c.1083C>A synonymous_variant 0.22
Rv3236c 3612070 c.1047G>T synonymous_variant 0.18
Rv3236c 3612651 p.Val156Leu missense_variant 0.15
Rv3236c 3612822 p.Leu99Ile missense_variant 0.15
Rv3236c 3612968 p.Gly50Glu missense_variant 0.22
Rv3236c 3613254 c.-138T>C upstream_gene_variant 0.12
fbiB 3641978 c.444C>T synonymous_variant 0.17
fbiB 3642359 c.825C>A synonymous_variant 0.2
alr 3840296 c.1125G>T synonymous_variant 0.18
alr 3840349 p.Ala358Ser missense_variant 0.17
alr 3840452 c.969C>T synonymous_variant 0.19
rpoA 3877798 p.Ser237* stop_gained 0.2
rpoA 3878058 c.450G>T synonymous_variant 0.17
rpoA 3878174 p.Pro112Ser missense_variant 0.2
rpoA 3878177 p.Val111Met missense_variant 0.2
rpoA 3878178 p.Ile110Thr missense_variant 0.2
rpoA 3878182 p.Asp109Gly missense_variant 0.2
ddn 3987044 c.201G>A synonymous_variant 0.18
ddn 3987054 p.Gly71Arg missense_variant 0.2
clpC1 4038171 p.Pro845Leu missense_variant 0.18
clpC1 4038344 p.Glu787Asp missense_variant 0.15
clpC1 4039100 c.1605C>T synonymous_variant 0.2
clpC1 4039372 p.Glu445* stop_gained 0.2
clpC1 4039550 c.1155G>T synonymous_variant 0.18
clpC1 4039564 p.Ala381Ser missense_variant 0.22
clpC1 4040071 p.Pro212Thr missense_variant 0.29
clpC1 4040491 p.Gln72* stop_gained 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 0.92
clpC1 4040894 c.-190G>A upstream_gene_variant 0.2
panD 4044380 c.-99C>A upstream_gene_variant 0.18
panD 4044431 c.-150G>T upstream_gene_variant 0.2
panD 4044474 c.-193C>T upstream_gene_variant 0.18
embC 4240391 p.Ala177Ser missense_variant 0.17
embC 4240639 c.777C>T synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241291 p.Leu477Met missense_variant 0.17
embC 4241717 c.1855C>A synonymous_variant 0.18
embC 4241982 p.Pro707Arg missense_variant 0.2
embC 4242095 p.Ala745Ser missense_variant 0.2
embA 4242367 c.-866C>A upstream_gene_variant 0.22
embA 4242385 c.-848C>T upstream_gene_variant 0.18
embC 4242399 p.Ala846Asp missense_variant 0.18
embC 4242419 p.Ser853Gly missense_variant 0.15
embA 4242433 c.-800C>A upstream_gene_variant 0.17
embC 4242473 p.Leu871Met missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243661 c.429C>A synonymous_variant 0.22
embA 4243707 p.Ala159Ser missense_variant 0.18
embA 4245088 p.Ser619* stop_gained 0.21
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247790 p.Ser426Ile missense_variant 0.18
embB 4247846 p.Gln445Lys missense_variant 0.29
embB 4248382 c.1869C>A synonymous_variant 0.18
embB 4249528 c.3015C>A synonymous_variant 0.29
aftB 4267035 p.Arg601His missense_variant 0.25
aftB 4267939 p.Arg300Trp missense_variant 0.22
aftB 4268201 c.636G>T synonymous_variant 0.18
aftB 4268617 p.Gly74Cys missense_variant 0.25
aftB 4268886 c.-50G>T upstream_gene_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.94
ethA 4326012 p.Gly488Trp missense_variant 0.27
ethA 4326136 c.1338G>T synonymous_variant 0.17
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327511 c.-38C>T upstream_gene_variant 0.18
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.94
gid 4407848 p.Ala119Thr missense_variant 1.0
gid 4407856 p.Arg116Leu missense_variant 0.2
gid 4407873 c.330G>T synonymous_variant 1.0