Run ID: SRR15014682
Sample name:
Date: 03-04-2023 12:35:17
Number of reads: 1789606
Percentage reads mapped: 99.07
Strain: lineage4.8
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.92 | rifampicin |
katG | 2156110 | p.Val1Ala | missense_variant | 1.0 | isoniazid |
embB | 4247429 | p.Met306Leu | missense_variant | 0.64 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7484 | c.183T>C | synonymous_variant | 0.12 |
gyrA | 7490 | c.189C>A | synonymous_variant | 0.12 |
gyrA | 7496 | c.195C>G | synonymous_variant | 0.11 |
gyrA | 7523 | c.222C>G | synonymous_variant | 0.13 |
gyrA | 7526 | c.225G>C | synonymous_variant | 0.13 |
gyrA | 7541 | c.240C>G | synonymous_variant | 0.13 |
gyrA | 7556 | c.255C>T | synonymous_variant | 0.13 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.12 |
gyrA | 7592 | c.291G>C | synonymous_variant | 0.14 |
gyrA | 7595 | c.294C>G | synonymous_variant | 0.13 |
gyrA | 7601 | c.300C>G | synonymous_variant | 0.12 |
gyrA | 7631 | c.330G>T | synonymous_variant | 0.13 |
gyrA | 7637 | c.336C>T | synonymous_variant | 0.13 |
gyrA | 7652 | c.351C>T | synonymous_variant | 0.12 |
gyrA | 7658 | c.357A>G | synonymous_variant | 0.12 |
gyrA | 7664 | c.363T>C | synonymous_variant | 0.12 |
mshA | 576347 | p.Thr334Ala | missense_variant | 1.0 |
rpoC | 766540 | p.Asp1057Glu | missense_variant | 0.12 |
rpoC | 766570 | c.3201T>C | synonymous_variant | 0.12 |
rpoC | 766573 | c.3204T>G | synonymous_variant | 0.12 |
rpoC | 766585 | c.3216T>C | synonymous_variant | 0.12 |
rpoC | 766900 | c.3531T>C | synonymous_variant | 0.11 |
rpoC | 766942 | c.3573C>T | synonymous_variant | 0.13 |
rpoC | 766945 | c.3576A>G | synonymous_variant | 0.13 |
rpoC | 766963 | c.3594T>C | synonymous_variant | 0.15 |
rpoC | 766972 | c.3603G>C | synonymous_variant | 0.15 |
rpoC | 766996 | c.3627C>T | synonymous_variant | 0.13 |
rpoC | 767033 | p.Ser1222Arg | missense_variant | 0.12 |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.11 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472978 | n.1133T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289652 | c.-411C>A | upstream_gene_variant | 1.0 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
Rv3083 | 3448500 | c.-4A>G | upstream_gene_variant | 1.0 |
Rv3083 | 3448501 | c.-3G>T | upstream_gene_variant | 1.0 |
rpoA | 3878061 | c.447G>C | synonymous_variant | 0.12 |
rpoA | 3878070 | c.438T>C | synonymous_variant | 0.11 |
rpoA | 3878082 | c.426T>G | synonymous_variant | 0.11 |
rpoA | 3878085 | c.423G>A | synonymous_variant | 0.12 |
rpoA | 3878106 | c.402G>C | synonymous_variant | 0.11 |
rpoA | 3878143 | p.Gly122Asp | missense_variant | 0.11 |
rpoA | 3878548 | c.-41C>T | upstream_gene_variant | 0.15 |
clpC1 | 4038743 | c.1962G>A | synonymous_variant | 0.14 |
clpC1 | 4038755 | c.1950G>C | synonymous_variant | 0.14 |
clpC1 | 4038764 | c.1941C>G | synonymous_variant | 0.14 |
clpC1 | 4038773 | c.1932T>C | synonymous_variant | 0.14 |
clpC1 | 4038790 | c.1915C>T | synonymous_variant | 0.15 |
clpC1 | 4038812 | c.1893T>C | synonymous_variant | 0.15 |
clpC1 | 4038838 | c.1867C>T | synonymous_variant | 0.18 |
clpC1 | 4038854 | c.1851G>A | synonymous_variant | 0.17 |
clpC1 | 4038857 | c.1848C>T | synonymous_variant | 0.17 |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.19 |
clpC1 | 4038884 | c.1821C>T | synonymous_variant | 0.19 |
clpC1 | 4038896 | c.1809C>T | synonymous_variant | 0.2 |
clpC1 | 4038908 | c.1797C>G | synonymous_variant | 0.19 |
clpC1 | 4038911 | c.1794G>A | synonymous_variant | 0.2 |
clpC1 | 4038914 | c.1791G>C | synonymous_variant | 0.2 |
clpC1 | 4038923 | c.1780_1782delCTAinsTTG | synonymous_variant | 0.19 |
clpC1 | 4038953 | c.1752A>G | synonymous_variant | 0.19 |
clpC1 | 4038965 | c.1740T>C | synonymous_variant | 0.18 |
clpC1 | 4038971 | c.1734T>C | synonymous_variant | 0.16 |
clpC1 | 4038974 | c.1731T>C | synonymous_variant | 0.16 |
clpC1 | 4038989 | c.1716T>C | synonymous_variant | 0.16 |
clpC1 | 4039022 | c.1683A>G | synonymous_variant | 0.12 |
clpC1 | 4039064 | c.1641C>G | synonymous_variant | 0.11 |
clpC1 | 4040387 | c.318A>G | synonymous_variant | 0.13 |
clpC1 | 4040393 | c.312G>C | synonymous_variant | 0.13 |
clpC1 | 4040402 | c.303C>T | synonymous_variant | 0.13 |
clpC1 | 4040411 | c.294T>C | synonymous_variant | 0.13 |
clpC1 | 4040423 | c.282A>G | synonymous_variant | 0.14 |
clpC1 | 4040431 | c.274T>C | synonymous_variant | 0.17 |
clpC1 | 4040441 | c.264C>G | synonymous_variant | 0.17 |
clpC1 | 4040444 | c.261C>T | synonymous_variant | 0.18 |
clpC1 | 4040450 | c.255A>G | synonymous_variant | 0.18 |
clpC1 | 4040456 | c.249C>T | synonymous_variant | 0.19 |
clpC1 | 4040459 | c.246C>G | synonymous_variant | 0.19 |
clpC1 | 4040471 | c.234T>C | synonymous_variant | 0.17 |
clpC1 | 4040477 | c.228G>T | synonymous_variant | 0.16 |
clpC1 | 4040480 | c.225T>G | synonymous_variant | 0.16 |
clpC1 | 4040507 | c.198C>T | synonymous_variant | 0.83 |
clpC1 | 4040522 | c.183T>C | synonymous_variant | 0.15 |
clpC1 | 4040528 | c.177G>C | synonymous_variant | 0.14 |
clpC1 | 4040531 | c.174T>C | synonymous_variant | 0.15 |
clpC1 | 4040546 | c.159G>A | synonymous_variant | 0.14 |
clpC1 | 4040551 | c.154T>C | synonymous_variant | 0.14 |
clpC1 | 4040561 | c.144A>G | synonymous_variant | 0.14 |
clpC1 | 4040567 | c.138C>G | synonymous_variant | 0.13 |
clpC1 | 4040573 | c.132T>C | synonymous_variant | 0.13 |
clpC1 | 4040582 | c.123G>T | synonymous_variant | 0.12 |
clpC1 | 4040591 | c.114C>T | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |