TB-Profiler result

Run: SRR4035714
Summary

Run ID: SRR4035714

Sample name:

Date: 04-04-2023 07:15:12

Number of reads: 755434

Percentage reads mapped: 99.43

Strain: lineage4.1.2

Drug-resistance: Other

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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
tlyA 1918586 c.649delG frameshift_variant 0.18 capreomycin
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 5291 p.Thr18Ala missense_variant 0.11
gyrB 5472 p.Ala78Val missense_variant 0.25
gyrB 6080 p.Lys281Glu missense_variant 0.25
gyrB 6088 c.849C>T synonymous_variant 0.25
gyrB 6273 p.Leu345His missense_variant 0.18
gyrA 6307 c.-995T>A upstream_gene_variant 0.18
gyrA 6346 c.-956C>G upstream_gene_variant 0.2
gyrB 6567 p.Ala443Val missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7831 p.Gly177Glu missense_variant 0.29
gyrA 7988 c.688delA frameshift_variant 0.22
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8567 c.1266C>T synonymous_variant 0.17
gyrA 8682 p.Glu461Lys missense_variant 0.18
gyrA 8688 p.Ala463Pro missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490971 c.189A>G synonymous_variant 0.2
fgd1 490985 p.Leu68Pro missense_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491607 c.825G>A synonymous_variant 0.18
fgd1 491664 c.882C>T synonymous_variant 0.2
mshA 575168 c.-180C>T upstream_gene_variant 0.22
mshA 575200 c.-148T>C upstream_gene_variant 0.25
mshA 575238 c.-110T>A upstream_gene_variant 0.18
mshA 575319 c.-29C>T upstream_gene_variant 0.25
mshA 575379 p.Gly11Val missense_variant 0.29
mshA 576190 p.Asp281Glu missense_variant 0.25
ccsA 619709 c.-182T>A upstream_gene_variant 0.22
ccsA 619784 c.-107G>T upstream_gene_variant 0.15
ccsA 619787 c.-104_-103insAG upstream_gene_variant 0.17
ccsA 620606 p.Val239Ala missense_variant 0.14
ccsA 620657 p.Gly256Asp missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760197 p.Ala131Thr missense_variant 0.17
rpoB 762233 c.2427G>A synonymous_variant 0.15
rpoC 763958 p.Val197Ile missense_variant 0.2
rpoC 763974 p.Glu202Val missense_variant 0.18
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764537 p.Pro390Ser missense_variant 0.29
rpoC 764717 p.Glu450Gln missense_variant 0.13
rpoC 764750 p.Val461Leu missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765161 c.1794delA frameshift_variant 0.13
rpoC 765226 p.Ile619Met missense_variant 0.1
rpoC 765516 p.Leu716Pro missense_variant 0.18
rpoC 765726 p.Gly786Ala missense_variant 0.12
rpoC 765960 p.Ala864Glu missense_variant 0.15
rpoC 766402 c.3033C>A synonymous_variant 0.13
rpoC 766429 c.3060C>A synonymous_variant 0.18
rpoC 766434 p.Glu1022Val missense_variant 0.15
rpoC 766788 p.Glu1140Gly missense_variant 0.18
rpoC 766857 p.Arg1163His missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775651 c.2830C>A synonymous_variant 0.2
mmpL5 776283 p.Ala733Val missense_variant 0.2
mmpL5 776866 p.Met539Leu missense_variant 0.18
mmpL5 776877 p.Gln535Leu missense_variant 0.22
mmpL5 776899 p.Asp528His missense_variant 0.18
mmpL5 777130 p.Glu451Lys missense_variant 0.29
mmpL5 777139 c.1342C>T synonymous_variant 0.25
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777730 c.749_750delTC frameshift_variant 0.25
mmpL5 777982 p.Glu167Lys missense_variant 0.29
mmpR5 779348 p.Val120Ala missense_variant 0.2
mmpR5 779380 p.Gln131* stop_gained 0.22
mmpS5 779565 c.-660G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801003 c.195G>A synonymous_variant 0.18
rplC 801080 p.Ala91Asp missense_variant 0.18
rplC 801087 c.279C>A synonymous_variant 0.2
rplC 801098 p.Val97Asp missense_variant 0.2
rplC 801113 p.Thr102Asn missense_variant 0.2
fbiC 1302832 c.-99G>C upstream_gene_variant 0.12
fbiC 1303206 c.276C>T synonymous_variant 0.15
fbiC 1303341 c.413delT frameshift_variant 0.15
fbiC 1303545 c.617dupC frameshift_variant 0.33
fbiC 1304074 p.Ala382Thr missense_variant 0.2
fbiC 1305234 c.2304G>C synonymous_variant 0.33
Rv1258c 1406339 c.1002C>T synonymous_variant 0.17
Rv1258c 1407205 p.Ile46Val missense_variant 0.13
Rv1258c 1407522 c.-182C>T upstream_gene_variant 0.15
embR 1416822 p.Ala176Thr missense_variant 0.14
embR 1416887 p.Arg154Leu missense_variant 0.15
embR 1416938 c.409dupC frameshift_variant 0.25
atpE 1461026 c.-19C>T upstream_gene_variant 0.15
atpE 1461189 c.145C>T synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471926 n.81C>A non_coding_transcript_exon_variant 0.4
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.22
rrs 1472547 n.703delA non_coding_transcript_exon_variant 0.2
rrl 1473735 n.78T>A non_coding_transcript_exon_variant 0.15
rrl 1474955 n.1298T>C non_coding_transcript_exon_variant 0.5
rrl 1474963 n.1306G>A non_coding_transcript_exon_variant 0.29
rrl 1475490 n.1833C>T non_coding_transcript_exon_variant 0.2
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.33
rrl 1476509 n.2852A>G non_coding_transcript_exon_variant 0.25
rrl 1476517 n.2860C>G non_coding_transcript_exon_variant 0.29
inhA 1673366 c.-836G>A upstream_gene_variant 0.25
fabG1 1673464 p.Ala9Thr missense_variant 0.33
fabG1 1673733 p.Met98Ile missense_variant 0.22
fabG1 1673837 p.Gly133Asp missense_variant 0.4
fabG1 1673845 p.Ile136Leu missense_variant 0.29
inhA 1673919 c.-283G>A upstream_gene_variant 0.18
inhA 1674273 c.72C>T synonymous_variant 0.15
inhA 1674287 p.Ala29Val missense_variant 0.14
inhA 1674468 c.271dupG frameshift_variant 0.18
inhA 1674523 p.Phe108Leu missense_variant 0.18
inhA 1674790 c.589C>T synonymous_variant 0.3
inhA 1674855 c.654C>A synonymous_variant 0.25
rpsA 1833447 c.-95C>T upstream_gene_variant 0.25
rpsA 1833473 c.-69C>T upstream_gene_variant 0.25
rpsA 1833507 c.-35C>T upstream_gene_variant 0.29
rpsA 1833516 c.-26A>C upstream_gene_variant 0.29
rpsA 1833524 c.-18C>T upstream_gene_variant 0.29
rpsA 1833786 p.Val82Ala missense_variant 0.13
rpsA 1833791 p.Asp84Asn missense_variant 0.13
rpsA 1833797 p.Val86Leu missense_variant 0.12
rpsA 1833800 p.Glu87* stop_gained 0.13
rpsA 1833899 p.Lys120* stop_gained 0.14
rpsA 1833964 c.423C>T synonymous_variant 0.17
rpsA 1833992 p.Ser151Thr missense_variant 0.2
rpsA 1834217 p.Val226Ile missense_variant 0.25
rpsA 1834309 c.768C>T synonymous_variant 0.14
rpsA 1834559 p.Val340Ile missense_variant 0.18
rpsA 1834813 c.1272G>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918565 p.Leu209His missense_variant 0.13
ndh 2102213 p.Ser277* stop_gained 0.22
ndh 2102228 p.Ala272Val missense_variant 0.2
ndh 2102238 p.Ile269Val missense_variant 0.18
ndh 2102272 c.771C>T synonymous_variant 0.17
ndh 2102290 c.753C>T synonymous_variant 0.18
ndh 2102345 p.Ala233Gly missense_variant 0.17
ndh 2102364 p.Lys227* stop_gained 0.15
ndh 2102678 p.Gly122Ala missense_variant 0.17
ndh 2102696 p.Ile116Thr missense_variant 0.14
ndh 2102956 c.87G>A synonymous_variant 0.18
ndh 2103224 c.-182C>T upstream_gene_variant 0.4
katG 2154100 p.Ser671Leu missense_variant 0.25
katG 2154297 c.1815G>A synonymous_variant 0.18
katG 2156159 c.-48C>A upstream_gene_variant 0.5
PPE35 2167671 p.Phe981Ser missense_variant 0.22
PPE35 2167690 p.Asn975Tyr missense_variant 0.2
PPE35 2169055 c.1557delA frameshift_variant 0.18
PPE35 2169106 p.Leu503Met missense_variant 0.29
PPE35 2169236 p.Asp459Glu missense_variant 0.12
PPE35 2170304 c.309G>T synonymous_variant 0.15
Rv1979c 2222039 p.Gly376Ser missense_variant 0.13
Rv1979c 2222798 p.Pro123Ala missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223325 c.-161G>T upstream_gene_variant 0.14
Rv1979c 2223336 c.-172G>A upstream_gene_variant 0.15
pncA 2289098 p.Lys48Asn missense_variant 0.29
pncA 2289331 c.-90C>T upstream_gene_variant 0.2
pncA 2289367 c.-126C>T upstream_gene_variant 0.29
kasA 2518040 c.-75G>A upstream_gene_variant 0.18
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518574 p.Ile154Val missense_variant 0.18
kasA 2518581 p.Leu156Gln missense_variant 0.18
kasA 2518590 p.Gly159Glu missense_variant 0.2
eis 2714206 p.Arg376His missense_variant 0.2
eis 2714827 p.Thr169Ile missense_variant 0.18
eis 2715433 c.-101T>C upstream_gene_variant 0.22
ahpC 2726541 p.Glu117Gln missense_variant 0.2
folC 2747344 c.255G>A synonymous_variant 0.25
pepQ 2860155 c.264C>T synonymous_variant 0.29
pepQ 2860254 c.165C>T synonymous_variant 0.25
pepQ 2860339 p.Leu27Pro missense_variant 0.17
pepQ 2860489 c.-71G>A upstream_gene_variant 0.15
pepQ 2860556 c.-138C>T upstream_gene_variant 0.18
ribD 2986884 c.46C>T synonymous_variant 0.15
ribD 2987121 p.Gly95Cys missense_variant 0.2
Rv2752c 3064729 p.Ala488Val missense_variant 0.14
Rv2752c 3066133 p.Ala20Val missense_variant 0.17
Rv2752c 3066377 c.-186G>A upstream_gene_variant 0.17
thyX 3067438 p.Ala170Thr missense_variant 0.29
thyX 3067707 p.Phe80Ser missense_variant 0.22
thyX 3067730 c.216G>A synonymous_variant 0.18
thyX 3067760 c.186G>A synonymous_variant 0.23
thyX 3067800 p.Lys49Met missense_variant 0.13
thyA 3074509 c.-38G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338923 c.-195T>A upstream_gene_variant 0.18
fbiD 3338927 c.-191C>T upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474628 p.Thr208Ala missense_variant 0.29
fprA 3474635 p.Leu210* stop_gained 0.2
fprA 3474645 c.639C>T synonymous_variant 0.22
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612355 p.Glu254Asp missense_variant 0.18
Rv3236c 3612688 c.429C>A synonymous_variant 0.25
Rv3236c 3613135 c.-19G>A upstream_gene_variant 0.17
Rv3236c 3613269 c.-153C>T upstream_gene_variant 0.25
fbiA 3640346 c.-197G>T upstream_gene_variant 0.18
fbiA 3640484 c.-59T>C upstream_gene_variant 0.2
fbiA 3640573 p.Gly11Arg missense_variant 0.33
fbiB 3641642 c.108G>A synonymous_variant 0.17
fbiB 3642100 p.Val189Ala missense_variant 0.22
fbiB 3642174 p.Val214Leu missense_variant 0.17
fbiB 3642413 c.879G>A synonymous_variant 0.18
fbiB 3642534 c.1000C>A synonymous_variant 0.15
fbiB 3642570 p.Glu346* stop_gained 0.17
fbiB 3642623 c.1089C>T synonymous_variant 0.29
alr 3840660 p.Gly254Asp missense_variant 0.2
alr 3840940 c.480delC frameshift_variant 0.22
alr 3840983 c.438C>T synonymous_variant 0.14
alr 3841154 c.267C>T synonymous_variant 0.25
alr 3841309 p.Ala38Thr missense_variant 0.15
alr 3841488 c.-68C>T upstream_gene_variant 0.33
rpoA 3878421 c.86delG frameshift_variant 0.2
clpC1 4038432 p.Leu758Gln missense_variant 0.18
clpC1 4038536 c.2169C>T synonymous_variant 0.22
clpC1 4040196 p.Val170Ala missense_variant 0.17
clpC1 4040626 p.Tyr27His missense_variant 0.33
embC 4239958 c.96C>T synonymous_variant 0.2
embC 4240102 c.243_247delCTTGA frameshift_variant 0.29
embC 4240379 p.Gln173* stop_gained 0.25
embC 4241058 p.Glu399Val missense_variant 0.22
embC 4241401 p.Phe513Leu missense_variant 0.29
embC 4241585 c.1725dupC frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242910 p.Phe1016Leu missense_variant 0.25
embC 4243139 p.Arg1093Ser missense_variant 0.15
embA 4243400 c.168C>A synonymous_variant 0.15
embA 4244296 p.Ala355Val missense_variant 0.29
embA 4244462 c.1230A>G synonymous_variant 0.17
embA 4245382 p.Thr717Asn missense_variant 0.18
embA 4245481 p.Leu750Gln missense_variant 0.22
embA 4245942 p.Arg904Ser missense_variant 0.22
embB 4245954 c.-560C>T upstream_gene_variant 0.17
embB 4246001 c.-513C>A upstream_gene_variant 0.14
embB 4248519 p.Ser669Ile missense_variant 0.2
embB 4249427 p.Arg972Cys missense_variant 0.5
aftB 4267186 p.Pro551Ser missense_variant 0.29
aftB 4267990 p.Ala283Thr missense_variant 0.29
aftB 4268868 c.-32G>T upstream_gene_variant 0.18
ubiA 4269160 p.Ser225Leu missense_variant 0.12
aftB 4269348 c.-512C>T upstream_gene_variant 0.15
ubiA 4269855 c.-22G>T upstream_gene_variant 0.4
ethA 4326229 c.1245C>T synonymous_variant 0.18
ethA 4326983 p.Pro164Arg missense_variant 0.5
ethA 4327541 c.-68G>T upstream_gene_variant 0.15
whiB6 4338198 c.324C>T synonymous_variant 0.25
whiB6 4338229 p.Leu98Pro missense_variant 0.25
whiB6 4338556 c.-35A>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338602 c.-81A>G upstream_gene_variant 0.15
whiB6 4338676 c.-155T>G upstream_gene_variant 0.12
gid 4407743 p.Arg154Trp missense_variant 0.13
gid 4407830 p.Gln125Glu missense_variant 0.11
gid 4408035 c.168T>C synonymous_variant 0.15
gid 4408207 c.-5G>T upstream_gene_variant 0.17