TB-Profiler result

Run: SRR13837507
Summary

Run ID: SRR13837507

Sample name:

Date: 03-04-2023 09:12:01

Number of reads: 589605

Percentage reads mapped: 95.32

Strain: lineage4.9

Drug-resistance: HR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
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
katG 2155411 p.Gly234Glu missense_variant 1.0 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
mshA 576259 c.912C>T synonymous_variant 1.0
ccsA 620690 p.Val267Glu missense_variant 1.0
rpoB 759805 c.-2T>C upstream_gene_variant 1.0
rpoB 761006 c.1200C>G synonymous_variant 0.1
rpoB 761015 c.1209G>C synonymous_variant 0.1
rpoB 761027 c.1221A>C synonymous_variant 0.11
rpoB 761051 c.1245G>T synonymous_variant 0.11
rpoB 761054 c.1248G>C synonymous_variant 0.11
rpoB 761057 c.1251G>C synonymous_variant 0.11
rpoB 761060 c.1254C>G synonymous_variant 0.1
rpoB 761063 c.1257C>G synonymous_variant 0.1
rpoB 761961 p.Pro719Thr missense_variant 0.95
rpoC 763031 c.-339T>G upstream_gene_variant 0.15
rpoC 763034 c.-336C>G upstream_gene_variant 0.15
rpoC 763040 c.-330C>G upstream_gene_variant 0.17
rpoC 763070 c.-300T>C upstream_gene_variant 0.15
rpoC 763082 c.-288C>T upstream_gene_variant 0.15
rpoC 763088 c.-282C>G upstream_gene_variant 0.14
rpoC 763094 c.-276G>C upstream_gene_variant 0.19
rpoC 763127 c.-243G>C upstream_gene_variant 0.11
rpoC 763546 c.177A>G synonymous_variant 0.1
rpoC 763570 c.201G>C synonymous_variant 0.11
rpoC 763594 c.225C>T synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.1
rpoC 763666 c.297G>C synonymous_variant 0.1
rpoC 764815 c.1446A>G synonymous_variant 0.14
rpoC 764824 c.1455T>C synonymous_variant 0.13
rpoC 764869 c.1500C>T synonymous_variant 0.11
rpoC 764875 c.1506C>A synonymous_variant 0.12
rpoC 764887 c.1518G>C synonymous_variant 0.12
rpoC 764888 c.1519T>C synonymous_variant 0.12
rpoC 764895 p.Ile509Thr missense_variant 0.89
rpoC 764911 c.1542A>G synonymous_variant 0.11
rpoC 764912 p.Met515Gln missense_variant 0.11
rpoC 764932 c.1563C>A synonymous_variant 0.11
rpoC 766846 c.3477C>A synonymous_variant 0.13
rpoC 766858 c.3489C>T synonymous_variant 0.12
rpoC 766861 c.3492G>C synonymous_variant 0.12
rpoC 766867 c.3498C>G synonymous_variant 0.13
rpoC 766876 c.3507C>T synonymous_variant 0.13
rpoC 766883 p.Ser1172Ala missense_variant 0.13
rpoC 766891 c.3522G>A synonymous_variant 0.14
rpoC 766894 c.3525T>C synonymous_variant 0.13
rpoC 766895 c.3526T>C synonymous_variant 0.13
rpoC 766900 c.3531T>C synonymous_variant 0.13
rpoC 766909 c.3540G>C synonymous_variant 0.13
rpoC 766911 p.Ile1181Thr missense_variant 0.13
rpoC 766915 p.Asp1182Glu missense_variant 0.12
rpoC 766918 c.3549C>T synonymous_variant 0.13
rpoC 766921 c.3552G>C synonymous_variant 0.12
rpoC 766931 p.Ala1188Ser missense_variant 0.12
rpoC 766942 c.3573C>T synonymous_variant 0.13
rpoC 766945 c.3576A>C synonymous_variant 0.13
mmpL5 777574 p.Phe303Leu missense_variant 1.0
mmpL5 777578 c.903C>G synonymous_variant 1.0
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0
rplC 801169 p.Lys121* stop_gained 1.0
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 0.95
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 0.9
tlyA 1918432 p.Pro165Thr missense_variant 1.0
ndh 2101769 p.Arg425His missense_variant 1.0
katG 2155508 p.Ala202Ser missense_variant 1.0
pncA 2289474 c.-233C>G upstream_gene_variant 1.0
folC 2746862 p.Leu246Arg missense_variant 1.0
folC 2747268 p.Asp111His missense_variant 1.0
Rv2752c 3065109 c.1083A>G synonymous_variant 1.0
fprA 3475241 p.Ala412Gly missense_variant 1.0
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0
rpoA 3877554 c.954G>A synonymous_variant 0.12
rpoA 3877560 c.948C>T synonymous_variant 0.12
rpoA 3877563 c.945C>T synonymous_variant 0.12
rpoA 3877569 c.939G>C synonymous_variant 0.11
rpoA 3877587 c.921A>G synonymous_variant 0.11
rpoA 3877593 c.915C>T synonymous_variant 0.1
rpoA 3877614 c.894G>A synonymous_variant 0.11
rpoA 3877620 c.888G>A synonymous_variant 0.11
rpoA 3877638 c.870T>C synonymous_variant 0.11
rpoA 3877656 c.852T>G synonymous_variant 0.11
rpoA 3877665 c.843C>G synonymous_variant 0.12
rpoA 3877677 c.831G>C synonymous_variant 0.17
rpoA 3877680 c.828G>C synonymous_variant 0.19
rpoA 3877686 c.822A>G synonymous_variant 0.12
rpoA 3877692 c.816G>C synonymous_variant 0.12
clpC1 4038468 p.Asp746Gly missense_variant 1.0
clpC1 4039472 c.1233G>C synonymous_variant 0.1
clpC1 4039478 c.1227G>C synonymous_variant 0.11
clpC1 4039481 c.1224T>C synonymous_variant 0.11
clpC1 4039487 c.1218G>C synonymous_variant 0.18
clpC1 4039528 c.1177C>A synonymous_variant 0.16
clpC1 4039541 c.1164C>G synonymous_variant 0.12
clpC1 4039544 c.1161C>T synonymous_variant 0.12
clpC1 4039559 c.1146C>G synonymous_variant 0.12
clpC1 4039565 c.1140G>T synonymous_variant 0.15
clpC1 4039570 p.Met379Leu missense_variant 0.14
clpC1 4039571 c.1134G>A synonymous_variant 0.13
clpC1 4039574 p.Ala377Gly missense_variant 0.13
clpC1 4039586 c.1119G>C synonymous_variant 0.15
clpC1 4039601 c.1104G>A synonymous_variant 0.15
clpC1 4039661 c.1044T>C synonymous_variant 0.18
clpC1 4039724 c.981A>G synonymous_variant 0.18
clpC1 4039733 c.972G>A synonymous_variant 0.17
clpC1 4039739 c.966C>G synonymous_variant 0.18
clpC1 4039742 c.963C>T synonymous_variant 0.18
clpC1 4039748 c.957G>C synonymous_variant 0.2
clpC1 4039751 c.954A>G synonymous_variant 0.2
clpC1 4039757 c.948A>G synonymous_variant 0.2
clpC1 4039760 c.945T>C synonymous_variant 0.2
clpC1 4039763 c.942C>T synonymous_variant 0.2
clpC1 4039769 c.936C>G synonymous_variant 0.2
clpC1 4039778 c.927A>G synonymous_variant 0.17
clpC1 4039793 c.912C>G synonymous_variant 0.17
clpC1 4040148 p.Lys186Ile missense_variant 1.0
clpC1 4040381 c.324T>C synonymous_variant 0.13
clpC1 4040387 c.318A>G synonymous_variant 0.14
clpC1 4040393 c.312G>C synonymous_variant 0.14
clpC1 4040411 c.294T>C synonymous_variant 0.12
clpC1 4040423 c.282A>G synonymous_variant 0.11
clpC1 4040426 c.279T>C synonymous_variant 0.12
clpC1 4040431 c.274T>C synonymous_variant 0.15
clpC1 4040441 c.264C>G synonymous_variant 0.14
clpC1 4040444 c.261C>G synonymous_variant 0.14
clpC1 4040450 c.255A>G synonymous_variant 0.14
clpC1 4040456 c.249C>T synonymous_variant 0.15
clpC1 4040459 c.246C>G synonymous_variant 0.16
clpC1 4040462 c.243C>T synonymous_variant 0.17
clpC1 4040465 c.240T>C synonymous_variant 0.16
clpC1 4040480 c.225T>C synonymous_variant 0.16
clpC1 4040495 c.210C>T synonymous_variant 0.15
clpC1 4040522 c.183T>C synonymous_variant 0.12
clpC1 4040531 c.174T>G synonymous_variant 0.11
clpC1 4040546 c.159G>C synonymous_variant 0.12
clpC1 4040558 c.147G>C synonymous_variant 0.13
clpC1 4040561 c.144A>G synonymous_variant 0.12
clpC1 4040573 c.132T>C synonymous_variant 0.12
embC 4240125 p.Cys88Tyr missense_variant 1.0
ethR 4327643 p.Thr32Ile missense_variant 1.0