Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,466,258	G→C	13.4%	pseudogene (867/2513 nt)	ydbA →	pseudogene, autotransporter homolog; interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,466,258	0	G	C	13.4%	105.1 / 6.9	43	pseudogene (867/2513 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base G (11/26);  new base C (3/3);  total (14/29)
Fisher's exact test for biased strand distribution p-value = 3.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGA  >  NC_000913/1466111‑1466398                                                                                                                                                    |                                                                                                                                             cGGTACGGAAATCAACGGTACTAACGGGCAAGTGATTCAGGACGGCGAGCTGCATGTCAGCGGCGGCGGTCACGGGATTGATATCACCGGCGACAGCGCGACGGGGGATAACAAGGGCACCATGACCGACACCGATCCGGAGGCCATgg                                                                                                                                             <  2:618479/149‑1 (MQ=11) cGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATgg                                                                                                                                             <  1:320612/149‑1 (MQ=40) cGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGAGCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATgg                                                                                                                                             <  1:106147/149‑1 (MQ=255)       ggAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCTGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATcc                                                                                                                                       <  1:24899/149‑1 (MQ=255)       ggAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGAGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATcc                                                                                                                                       >  2:929829/1‑149 (MQ=255)                  gTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGt                                                                                                                            <  1:1018565/149‑1 (MQ=255)                     ataaCGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGAc                                                                                                                         <  2:292014/149‑1 (MQ=255)                           ggAAAGGGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCTCCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGcc                                                                                                                   <  1:619524/149‑1 (MQ=255)                              acgTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATc                                                                                                                <  1:1020417/147‑1 (MQ=255)                                gTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGt                                                                                                              <  1:232340/149‑1 (MQ=255)                                         gcaggCGATCTGGACGTCAGCGGCGGCGGTCACGGTATTTATATCACCGGTGACAGCGCGACGGTTGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCTTGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGa                                                                                                     <  2:963366/146‑1 (MQ=14)                                               gATCTGGATGGTAGCGGCGGCGGTCTAGGTATTGATTTCACCGGTGACAGCGCGACGGTGGATATCAAGGGCACCATGTCCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCga                                                                                               <  2:714296/149‑1 (MQ=14)                                                        gTCAGCGGCGGCGGTCACGGTATTGATATCACCGCTGACAGCGCGACGGTGGATAACAAGTGCACCATGACCGTCACCGATCCCGAGTCCATGGGTATCCAGATCGAAGGTGACAAGGCCATCGTCAATAACGCAGGCGAGAGCACCaa                                                                                      >  2:967515/1‑148 (MQ=14)                                                          cAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCa                                                                                    >  1:430627/1‑149 (MQ=255)                                                          cAGCGGCGGCGGTCAAGGTTTTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCa                                                                                    <  2:990429/149‑1 (MQ=255)                                                           aGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGTCAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCAc                                                                                   >  1:637436/1‑149 (MQ=255)                                                            gcggcggcgGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATcc                                                                                                                                       >  2:202644/1‑96 (MQ=18)                                                                  gcggTCACGGTATTGATTTCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGGCTCCAGATCGACGGTGACAAGGCCATCGGCCATAACGAAGGCGAGAGCACCATCACCAACGGt                                                                            <  1:209995/149‑1 (MQ=17)                                                                   cggTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTg                                                                           <  2:536820/149‑1 (MQ=255)                                                                    gggcACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTgg                                                                          <  2:391338/146‑1 (MQ=255)                                                                       taCGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGTCGAGAGCACCATCACCAACGGTggcac                                                                       <  2:21205/148‑1 (MQ=255)                                                                          ggTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTggcaccgg                                                                    <  2:396665/149‑1 (MQ=255)                                                                            tATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTggcaccggca                                                                  <  2:200780/149‑1 (MQ=255)                                                                            tATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATc                                                                                                                                        <  1:753640/79‑1 (MQ=21)                                                                            tATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATc                                                                                                                                        >  2:753640/1‑79 (MQ=21)                                                                               tGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCAccc                                                               <  1:84540/149‑1 (MQ=255)                                                                                  tatCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTTTCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGa                                                            >  1:448347/1‑149 (MQ=255)                                                                                    tCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCa                                                                                                                                      >  1:82899/1‑73 (MQ=21)                                                                                    tCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCa                                                                                                                                      <  2:82899/73‑1 (MQ=21)                                                                                      aCCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTaa                                                        <  2:639283/149‑1 (MQ=255)                                                                                      aCCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTaa                                                        <  2:4547/149‑1 (MQ=255)                                                                                       ccGGGGACAGCGCGACGGTGGATAACAACGGCACCATGCCCGTCACCGATCCGGAGTCCAGGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAAt                                                       <  1:255947/149‑1 (MQ=255)                                                                                          gTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCACCGGTGGCACCGGCACCCAGATTAATggg                                                    >  1:1022229/1‑148 (MQ=255)                                                                                                  gcgACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGc                                            >  1:64135/1‑149 (MQ=255)                                                                                                     aCGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCAc                                         <  2:309027/149‑1 (MQ=255)                                                                                                      cGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACg                                        <  2:430627/149‑1 (MQ=255)                                                                                                      cGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACg                                        <  2:617063/149‑1 (MQ=255)                                                                                                           gATAACAAGGGCACCAGGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCaaa                                   <  1:660531/149‑1 (MQ=255)                                                                                                            aTAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAaac                                  >  1:650465/1‑149 (MQ=255)                                                                                                              aaCAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAaacaa                                <  1:96009/149‑1 (MQ=255)                                                                                                               aCAAGGGCACCATGACCGTCACCGATCCGGAGACCATGGGTATCCAGATCGACGGTGACAAGGGCATCGTCAATAACGAAGGCGAGCGCACCATCACCTACGGTGGCCCCGCCCCCCCGCTTAATGGTGATGACGCCCCGGCTaacaac                               >  2:94498/1‑149 (MQ=18)                                                                                                                   gggCACCAGGACCGTCACCGCGCCGGAGGCCATCGGTATCCAGATCGACGGGGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACg                           <  1:855293/149‑1 (MQ=17)                                                                                                                     gCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGc                         <  2:650465/149‑1 (MQ=255)                                                                                                                               cGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCTCCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCg               >  1:271910/1‑149 (MQ=255)                                                                                                                                     cGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACg         >  1:476406/1‑149 (MQ=255)                                                                                                                                            gAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCAGCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGa  <  2:609392/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                             CGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGA  >  NC_000913/1466111‑1466398

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑