Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	1,466,210	G→A	10.9%	pseudogene (819/2513 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_3_pae_tpiA	1,466,210	0	G	A	10.9%	96.2 / 3.5	44	pseudogene (819/2513 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base G (8/31);  new base A (3/2);  total (11/33)
Fisher's exact test for biased strand distribution p-value = 9.07e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

CAGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAAT  >  NC_000913_3_pae_tpiA/1466065‑1466345                                                                                                                                                  |                                                                                                                                         caGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGAAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACg                                                                                                                                       >  2:29443/1‑149 (MQ=255)   gTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGAACGGAAAACAACGGTAATACAGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAACGGCGGCGGTCCCGGTATTAGTATCACCGGTGACAGCCCGACGGt                                                                                                                                     >  2:349780/1‑149 (MQ=17)    tAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTg                                                                                                                                    <  1:212551/149‑1 (MQ=255)      aacaacCAAGGCAAAATCACCGTTGACGGTAAAGATGCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGACTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGTTATTGATATCACCGGTGACAGCGCGACGGTGGa                                                                                                                                  <  2:430391/149‑1 (MQ=14)      aacaacAATGGCAAAACCACCGTTGACGGTAAAGCTTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGAGCTGGATGTAAGCGGCGGCCGTCACGGTCTCGATATCACCCGTGCCCGCGCGACGGTggc                                                                                                                                  >  2:581182/1‑148 (MQ=17)            aagggCAAAACCACCGTTGACGGTAAAGATGCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACaa                                                                                                                            <  2:733321/146‑1 (MQ=255)                  aaaaCCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAc                                                                                                                      >  2:421281/1‑149 (MQ=255)                  aaaaCCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAc                                                                                                                      <  1:678075/149‑1 (MQ=255)                  aaaaCCACCGTTGACGGTAAAGATTCCACCGGTAAGGCAATCAAGGATTAGAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAc                                                                                                                      <  1:239167/149‑1 (MQ=14)                      ccaccGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATg                                                                                                                 <  1:488339/149‑1 (MQ=255)                       caccGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGAGACGGTGGATAACAAGGGCAA‑CATGa                                                                                                                <  2:105075/149‑1 (MQ=255)                           gTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGt                                                                                                            <  2:93301/149‑1 (MQ=255)                           gTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGt                                                                                                            <  1:158501/149‑1 (MQ=255)                                  gTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAggg                                                                                                                         <  2:629837/130‑1 (MQ=16)                                  gTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGATAACAAggg                                                                                                                         >  1:629837/1‑130 (MQ=255)                                   tAAAGATTCCACCGGTACGGCAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCCGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATc                                                                                                    <  1:247475/149‑1 (MQ=255)                                   tAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAATTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATAACCGGTGAAAGCGAGCCGGTAGATAACAAGGGCAC‑CATGACCGTCAcccgtc                                                                                                    >  1:280870/1‑145 (MQ=14)                                    aaaGATTCCACTGGTAGGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGTTGTCAGCGGCGGCGGTCACGGTATTGATATCACCGCTGACAGCGCGACGGTGTATTACAAGGGTTC‑CATGACCGTCACCGATcc                                                                                                   <  2:687720/149‑1 (MQ=14)                                     aaGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGCGACAGCGCAACGGTGGCTAACAAGGGCAC‑CATGACCGTCCCCGCTccc                                                                                                  >  2:57411/1‑148 (MQ=11)                                        aTTCCACCTGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAg                                                                                               <  1:195916/149‑1 (MQ=255)                                              ccGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACATGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATg                                                                                         <  2:580356/149‑1 (MQ=255)                                               cGGTACGGAAATCAACGTGAATAACGGGAAAGTGCTTCAGTACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATgg                                                                                        <  2:57416/149‑1 (MQ=255)                                               cGGTACGGAAATCAACGGTAATAACGGGAAAGCGATTCAGGACGGCGATCTGGCTGTCAGCGGCGGTGGTCAAGGTATTGATATCACCGGCGACAGGGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATgg                                                                                        <  2:437769/149‑1 (MQ=11)                                                    cGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATc                                                                                   <  1:565470/149‑1 (MQ=255)                                                    cGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGGGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATc                                                                                   <  1:469335/149‑1 (MQ=255)                                                         agcAACGGGAATAACGGGAAAGTGAGTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGAt                                                                              <  2:608553/147‑1 (MQ=255)                                                            aaCGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGa                                                                           <  1:624306/149‑1 (MQ=255)                                                             aCGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGAt                                                                                                     >  1:117893/1‑122 (MQ=255)                                                             aCGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCAACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGAt                                                                                                     <  2:117893/122‑1 (MQ=25)                                                                 taataaCGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTg                                                                      <  1:421281/149‑1 (MQ=255)                                                                             aGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACCA‑GGCACTTATGGCTGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCg                                                          >  1:168337/1‑149 (MQ=14)                                                                              gTGATTCAGGACGGCGATCGGGATGTCAGCGGCGGGGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGt                                                         <  2:35878/149‑1 (MQ=255)                                                                                             gATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCga                                          <  1:154021/149‑1 (MQ=255)                                                                                             gATCTGGATGTCAGCGGCGGCGGTCACGGTATAGATATCACCGGTGACAGCGCGAAGGAGGAAAACAAGGACAC‑CATGACCGTCACGGATCGGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCATTAACGAAGGCga                                          <  1:581182/149‑1 (MQ=14)                                                                                               tCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCgaga                                        <  1:613541/149‑1 (MQ=255)                                                                                                                gcggTGACGGTATTGGTATCACCGGTTACAGGGGGACGGGGGATACCAAGGGCAC‑CATGGCCGTCACCGATCCTGCGTTGATGGGTATCCAGATCGACGGTGACAATGGCATGGTCCTTAACGTAGGCGAGTGCACCATCACCGCCGGt                       <  2:698427/149‑1 (MQ=255)                                                                                                                gcggGCACGGTATTGATATCCCCGGGTACAGCGCGACTGTGGATAAAAAGCGCAC‑CATGACCGTCACCGTTCCAGAGTACATGGGTATCCAGATCGACGGTGACAATGCCATCGTGTATAACGAAGGCGAGAGCACCATCACCAACGGt                       <  2:698442/149‑1 (MQ=255)                                                                                                                  ggccACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTgg                     <  1:244803/146‑1 (MQ=255)                                                                                                                      aCGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGa                                                                                                >  1:689274/1‑70 (MQ=255)                                                                                                                      aCGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGa                                                                                                <  2:689274/70‑1 (MQ=255)                                                                                                                        ggTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTggcaccgg               <  1:35687/149‑1 (MQ=255)                                                                                                                             tGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCAccc          <  2:659873/149‑1 (MQ=255)                                                                                                                                    aCCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATTCGGAGTCCATGGGTATCCAGATTGACGGCGACCAGGCCGTCGTCAACAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTaa   >  2:689230/1‑149 (MQ=14)                                                                                                                                     ccGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCTGTTTCCATGGTTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAAt  <  1:349780/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                         CAGTAAACAACAATGGCAAAACCACCGTTGACGGTAAAGATTCCACCGGTACGGAAATCAACGGTAATAACGGGAAAGTGATTCAGGACGGCGATCTGGATGTCAGCGGCGGCGGTCACGGTATTGATATCACCGGTGACAGCGCGACGGTGGATAACAAGGGCAC‑CATGACCGTCACCGATCCGGAGTCCATGGGTATCCAGATCGACGGTGACAAGGCCATCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGTGGCACCGGCACCCAGATTAAT  >  NC_000913_3_pae_tpiA/1466065‑1466345

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑