Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	562,187	C→T	Q831* (CAG→TAG)	sfmD →	putative outer membrane export usher protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	562,187	0	C	T	100.0%	163.0 / NA	51	Q831* (CAG→TAG)	sfmD	putative outer membrane export usher protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/24);  total (27/24)

GTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATAAGATAA  >  NC_000913/562081‑562321                                                                                                           |                                                                                                                                       gTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCAtt                                                                                                        <  1:815098/139‑1 (MQ=255)  tttGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTg                                                                                                       <  2:1076509/139‑1 (MQ=255)   ttGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTgc                                                                                                      <  2:238101/139‑1 (MQ=255)      gATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   <  2:148579/139‑1 (MQ=255)                   ggAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCg                                                                                      >  1:1046652/1‑139 (MQ=255)                      aaaCAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAg                                                                                   >  2:551361/1‑139 (MQ=255)                       aaCAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCa                                                                                                          >  1:887357/1‑115 (MQ=255)                       aaCAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCa                                                                                                          <  2:887357/115‑1 (MQ=255)                        aCAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCa                                                                                 <  2:1046652/139‑1 (MQ=255)                           gTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAg                                                                              >  1:216921/1‑139 (MQ=255)                                         aGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCg                                                                <  1:551361/139‑1 (MQ=255)                                          gTATGGTGCGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGATGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGt                                                               <  1:660306/139‑1 (MQ=255)                                            aTGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCa                                                             >  1:992340/1‑139 (MQ=255)                                                tgggtgATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCa                                                                                                          >  2:170173/1‑90 (MQ=255)                                                tgggtgATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCa                                                                                                          <  1:170173/90‑1 (MQ=255)                                                  ggtgATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   <  2:270785/95‑1 (MQ=255)                                                  ggtgATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   >  1:270785/1‑95 (MQ=255)                                                     gatgaCGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTAttt                                                    >  2:360195/1‑139 (MQ=255)                                                      atgaCGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACg                                                                                                               >  1:572437/1‑79 (MQ=255)                                                      atgaCGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACg                                                                                                               <  2:572437/79‑1 (MQ=255)                                                       tgaCGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCg                                                  >  1:67345/1‑139 (MQ=255)                                                         aCGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   >  2:909084/1‑88 (MQ=255)                                                         aCGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   <  1:909084/88‑1 (MQ=255)                                                            ggCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGTATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTgcgc                                                                                                    >  1:947163/1‑84 (MQ=255)                                                            ggCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGTATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTgcgc                                                                                                    <  2:947163/84‑1 (MQ=255)                                                              cAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGttt                                           >  2:480961/1‑139 (MQ=255)                                                                 gTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGca                                        <  1:360195/139‑1 (MQ=255)                                                                 gTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGca                                        <  1:806809/139‑1 (MQ=255)                                                                            tggtgCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGc                             >  2:371022/1‑139 (MQ=255)                                                                             ggtgCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTgg                              >  1:1085811/1‑137 (MQ=255)                                                                             ggtgCGCCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTgg                              <  2:1085811/137‑1 (MQ=255)                                                                                 cgcCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACa                                                                        <  1:941865/91‑1 (MQ=255)                                                                                 cgcCATTGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACa                                                                        >  2:941865/1‑91 (MQ=255)                                                                                      ttGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGcaca                                      <  2:1007933/120‑1 (MQ=255)                                                                                      ttGTCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGcaca                                      >  1:1007933/1‑120 (MQ=255)                                                                                         tCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGca                                        >  1:602573/1‑115 (MQ=255)                                                                                         tCTGGTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGca                                        <  2:602573/115‑1 (MQ=255)                                                                                         tCTGGTGAATTACTGGTTTAGCGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAAt                >  2:283301/1‑139 (MQ=255)                                                                                             gTGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATc            >  1:579832/1‑139 (MQ=255)                                                                                              tGAATTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCa           >  2:112674/1‑139 (MQ=255)                                                                                                aaTTACTGGTTTAGTGGGGAGACGGCGCGAACTCACg                                                                                                               >  2:413394/1‑37 (MQ=255)                                                                                                aaTTACTGGTTTAGTGGGGAGACGGCGCGAACTCACg                                                                                                               <  1:413394/37‑1 (MQ=255)                                                                                                 aTTACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATa        <  2:67345/139‑1 (MQ=255)                                                                                                  ttACTGGTTTAGTGGGGAGACGGCACGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATa        >  2:10673/1‑138 (MQ=255)                                                                                                  ttACTGGTTTAGTGGGGAGACGGCACGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATa        <  1:10673/138‑1 (MQ=255)                                                                                                   tACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   >  2:109410/1‑46 (MQ=255)                                                                                                   tACTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCa                                                                                                   <  1:109410/46‑1 (MQ=255)                                                                                                     cTGGTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATAAGAt    >  2:1114323/1‑139 (MQ=255)                                                                                                       ggTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATc                                  <  2:949559/107‑1 (MQ=255)                                                                                                       ggTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATc                                  >  1:949559/1‑107 (MQ=255)                                                                                                       ggTTTAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATAAGATaa  >  1:810165/1‑139 (MQ=255)                                                                                                           |                                                                                                                                       GTTTGGATCACTGGTACGGGAAAACAGTACCGGAATAACCAGTATGGTGGGTGATGACGGGCAAGTTTATTTAAGTGGTGCGCCATTGTCTGGTGAATTACTGGTTCAGTGGGGAGACGGCGCGAACTCACGCTGCATTGCGCACTATGTATTGCCGAAGCAAAGCTTACAGCAAGCCGTCACTGTTATTTCGGCAGTTTGCACACATCCTGGCTCATAAAGGAAATTATCAATAAGATAA  >  NC_000913/562081‑562321

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑