Run ID: SRR1140691
Sample name:
Date: 02-04-2023 20:57:44
Number of reads: 2866201
Percentage reads mapped: 87.45
Strain: lineage4.6.1.2;lineage4.4.1.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.6 | Euro-American | T;LAM | None | 0.71 |
lineage4.4 | Euro-American | S;T | None | 0.29 |
lineage4.4.1 | Euro-American (S-type) | S;T | None | 0.28 |
lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 | 0.7 |
lineage4.6.1.2 | Euro-American | T2 | RD724 | 0.64 |
lineage4.4.1.1 | Euro-American | S;Orphans | None | 0.29 |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7539 | p.Thr80Ala | missense_variant | 0.77 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9276 | c.1975C>T | synonymous_variant | 0.76 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
rpoC | 764810 | p.Pro481Thr | missense_variant | 0.76 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303391 | p.Arg154His | missense_variant | 0.79 |
embR | 1416410 | p.Leu313Arg | missense_variant | 0.69 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1471896 | n.51T>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1471900 | n.55C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472094 | n.249T>A | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472102 | n.257G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472112 | n.267C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472113 | n.268T>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472122 | n.277G>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472575 | n.730C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.35 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1474830 | n.1173A>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474831 | n.1174A>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.31 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474902 | n.1245T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474913 | n.1256T>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475696 | n.2039T>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475703 | n.2046A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475707 | n.2050T>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475713 | n.2056C>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475716 | n.2059A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475722 | n.2065G>A | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.25 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.29 |
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475866 | n.2209T>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475869 | n.2212C>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476165 | n.2508T>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.49 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476573 | n.2916A>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102990 | p.Val18Ala | missense_variant | 0.22 |
katG | 2154349 | p.Glu588Gly | missense_variant | 0.28 |
katG | 2155541 | p.Trp191Gly | missense_variant | 0.88 |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 0.25 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
folC | 2746923 | p.Gly226Ser | missense_variant | 0.2 |
Rv2752c | 3065920 | p.Pro91Leu | missense_variant | 0.65 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.32 |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 0.24 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 0.23 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243692 | p.Gly154Ser | missense_variant | 0.2 |
embA | 4245055 | p.Thr608Asn | missense_variant | 0.78 |
embB | 4246904 | p.Val131Met | missense_variant | 0.26 |
ethA | 4327107 | p.His123Tyr | missense_variant | 0.79 |
ethR | 4328171 | p.Val208Ala | missense_variant | 0.7 |
ethA | 4328252 | c.-779T>G | upstream_gene_variant | 0.33 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |