Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,466,630	G→C	15.9%	pseudogene (1239/2513 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	1,466,630	0	G	C	15.9%	110.2 / 18.7	51	pseudogene (1239/2513 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base G (20/22);  new base C (4/4);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.67e-01

TGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGA  >  NC_000913/1466483‑1466779                                                                                                                                                    |                                                                                                                                                      tGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCa                                                                                                                                                     <  1:658153/150‑1 (MQ=255) tGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGCTAGTTAACTACGAAGGCGAGAGCTCAATCACCAAAGGAGGCACCGGCACGCa                                                                                                                                                     >  2:946747/1‑150 (MQ=14)   atatCACCGGCGACAGCGCTACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGTTTGACGGCGACAAGGCGTTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGa                                                                                                                                                   <  2:545837/150‑1 (MQ=14)          cGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACgg                                                                                                                                            <  1:811540/150‑1 (MQ=255)              gACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGACCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGtgat                                                                                                                                        >  2:222139/1‑150 (MQ=255)                 aGCGCTACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGAc                                                                                                                                     <  2:772931/150‑1 (MQ=255)                  gggctaCGGTGGATAACAAGGGCACGATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGTTAGACGGCGACCAGGCTGTTGTTAAAAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACg                                                                                                                                    <  2:1175700/145‑1 (MQ=14)                  gcgcAACGGTGGATAACAAGGGCACCATGACCGTCACCGCTCCGGAGTCCATCGGGATCCAGGTTGACGGCGCCCAGGCCGTTGTGAAATACGAAGGCGAGAGCGCGATCACCAACGGGGGCACCGGCACGCAGCTGAACGGTGAGGACg                                                                                                                                    >  2:1095462/1‑150 (MQ=14)                  gcgcAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACg                                                                                                                                    <  2:937288/150‑1 (MQ=255)                       aCGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCCCg                                                                                                                               >  2:628409/1‑150 (MQ=255)                          gTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTCACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCa                                                                                                                            >  2:731404/1‑150 (MQ=255)                             gATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAaac                                                                                                                         >  2:1063621/1‑150 (MQ=255)                              aTAACAAGGGCACCCTGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAaaca                                                                                                                        <  2:170637/150‑1 (MQ=255)                              aTAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCTGTATCCAGTTTGACGGAGACCAGGCGGTTGTTAAAAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAaaca                                                                                                                        <  2:622997/150‑1 (MQ=255)                                    aGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACg                                                                                                                  <  1:517250/150‑1 (MQ=255)                                    aGGGCACCATGACCGTCACCGATCCGGAGTCCATAGGTATCCACGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCCCCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACg                                                                                                                  >  2:1106925/1‑150 (MQ=255)                                      ggCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAAAAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGc                                                                                                                >  2:697368/1‑150 (MQ=255)                                       gCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTAGTGAACAACGAAGGCGAGAGCGCGATCACCAACGGCGGCACCGGCACGCAGATAAACGGTGAAGACGCCACCGCGAAAAACAAGGGCa                                                                                                               >  1:647066/1‑150 (MQ=14)                                                     aCCGATCCGGAGTCCATCGGTATCCAGTTGGACGGCGACAAGGCGTTAGTCAACAACGAAGGCGAGAGCTCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGAc                                                                                                 <  2:367835/150‑1 (MQ=14)                                                                gTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTc                                                                                      >  2:1309381/1‑150 (MQ=255)                                                                    aTCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCTCGGCAAACAACAACGGGAAAACCACCGTTGACGGCAAGGATTCCAcc                                                                                  <  1:1072529/150‑1 (MQ=255)                                                                     tCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAATGGTGGCACCGGCACGCAGAATAACGGTGATGCCGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGCCAAGGATACCTCCg                                                                                 >  2:217068/1‑150 (MQ=18)                                                                      cGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCgg                                                                                <  2:568759/150‑1 (MQ=255)                                                                               ggTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACACCGGCAAAACCACCGTTGACGGCAAGGATGCCACCGGTCCGGAAAt                                                                       >  1:872158/1‑150 (MQ=255)                                                                                ggtGATGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCTCCATCACCCCCGGTGGAACCGGCACGCAGATTAACGGTTATGACGCGAAGGAAAACAACAACGGAAAAACCACCGTTGACGGCACGGATTCGACGGGTGCGGaaagg                                                                      >  2:1216157/3‑148 (MQ=17)                                                                                      ggCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGc                                                                <  2:593273/150‑1 (MQ=255)                                                                                        cGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCaa                                                              >  2:19674/1‑150 (MQ=255)                                                                                           ccAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATaa                                                           >  2:18421/1‑150 (MQ=255)                                                                                            cAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTTGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAAc                                                          <  1:222139/150‑1 (MQ=255)                                                                                            cAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATAAACGGTGAAGACGCCACGGCAAAAAACAAAGGCAAAACCACAGTTGACGGAAAGGATTCCACCGGTACGAAAATAGCGGGCAAAAAc                                                          >  1:10356/1‑150 (MQ=17)                                                                                               gCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAAtcaacggt                                                                >  2:125934/1‑134 (MQ=255)                                                                                               gCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAAtcaacggt                                                                <  1:125934/141‑8 (MQ=255)                                                                                                   ttgttAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAgg                                                   >  2:741681/1‑150 (MQ=255)                                                                                                    tgttAACAACGAAGGCGAGAGCGCCATCACCAAAGGTGTCACCGGCACTCAGATCAAAGGTAAATACGCCACCGCGAATAACATAGGAAAAACCACTCTTGATGGAAATGATTCCTCGGGTACCAAAATCTCTGGCATTATCggcattgt                                                  >  2:697564/1‑144 (MQ=255)                                                                                                          caacGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCa                                            >  2:488406/1‑150 (MQ=255)                                                                                                             cGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGa                                         >  1:634341/1‑150 (MQ=255)                                                                                                                aGGCGAGAGCGCCATCACCAACTGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACgg                                      <  2:638085/150‑1 (MQ=255)                                                                                                                aGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACgg                                      <  2:394678/150‑1 (MQ=255)                                                                                                                 ggCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGAAATAACGGTAAGGTGATTCAGGACGGc                                     >  2:218558/1‑150 (MQ=11)                                                                                                                     agagCACCATCACCAACGGTGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATc                                 <  1:218558/150‑1 (MQ=255)                                                                                                                      gagCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCt                                <  1:19674/150‑1 (MQ=255)                                                                                                                        gcgcCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTgg                              <  1:1063621/150‑1 (MQ=255)                                                                                                                           ccATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATg                           <  1:1309381/150‑1 (MQ=255)                                                                                                                                        tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTTCGGAAATTGCTGGCAATAACGGGAAGGt                                                  <  1:152538/114‑1 (MQ=255)                                                                                                                                        tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGt                                                  <  1:148135/114‑1 (MQ=255)                                                                                                                                        tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGt                                                  >  2:148135/1‑114 (MQ=255)                                                                                                                                        tGGCACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGt                                                  >  2:152538/1‑114 (MQ=255)                                                                                                                                           cACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCa                                            <  2:1113909/117‑1 (MQ=255)                                                                                                                                           cACCGGCACCCAGATTAATGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCa                                            >  1:1113909/1‑117 (MQ=255)                                                                                                                                               ggCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGt       <  1:628409/150‑1 (MQ=255)                                                                                                                                               ggCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGt       <  1:1106925/150‑1 (MQ=255)                                                                                                                                                    gCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGa  <  1:731404/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                      TGATATCACCGGCGACAGCGCAACGGTGGATAACAAGGGCACCATGACCGTCACCGATCCGGAGTCCATCGGTATCCAGGTTGACGGCGACCAGGCGGTTGTTAACAACGAAGGCGAGAGCGCCATCACCAACGGTGGCACCGGCACGCAGATTAACGGTGATGACGCCACGGCAAACAACAACGGCAAAACCACCGTTGACGGCAAGGATTCCACCGGTACGGAAATTGCTGGCAATAACGGGAAGGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGA  >  NC_000913/1466483‑1466779

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: ‑