Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,357,836	G→A	7.8%	pseudogene (33/198 nt)	ypaA →	pseudogene, C‑terminal fragment, Transposase_31 family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,357,836	0	G	A	7.8%	152.8 / 2.6	51	pseudogene (33/198 nt)	ypaA	pseudogene, C‑terminal fragment, Transposase_31 family
Reads supporting (aligned to +/- strand):  ref base G (29/18);  new base A (2/2);  total (31/20)
Fisher's exact test for biased strand distribution p-value = 6.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCC  >  NC_000913/2357689‑2357977                                                                                                                                                    |                                                                                                                                              tATGCATCATAAAGCCATTAATATTGCTTCTCTCATTCTTTATCAGGGCCTTGTACGTGAGATCTTGCTGTCGACAAGCCAAATCTATGATGCTGATCATCCGAACCGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTg                                                                                                                                               <  8:56553/148‑1 (MQ=255)         aaCAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCagga                                                                                                                                       <  8:340332/148‑1 (MQ=255)           cAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCaggaagg                                                                                                                                    <  4:69227/149‑1 (MQ=255)              gCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGAc                                                                                                                                  >  1:169160/1‑148 (MQ=255)                 aTTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGGACGTGAGATTGTGCTGGCGGCAACCCAGCTAAGGGAAGCTGATCTTGCGGAGTGTCAGAAATAGGTGAGAGTGGGGCCGATCGGTGACCGGCTGCGGCAGGGAGGACGTct                                                                                                                              >  7:359448/1‑148 (MQ=9)                 aTTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATc                                                                                                                               >  1:353476/1‑148 (MQ=255)                     aaaTTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAAtt                                                                                                                          <  2:169160/149‑1 (MQ=255)                     aaaTTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAAt                                                                                                                           <  8:58504/148‑1 (MQ=255)                     aaaTTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAAt                                                                                                                           <  2:353476/148‑1 (MQ=255)                       aTTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATtgg                                                                                                                        >  7:55355/1‑149 (MQ=255)                                cgcATGCTGGAGCAGGGCTTTGAACGTGACATTGTGCTGGCGACCACCCACCTCACAGAAGCAGATATTCAGAACTGTCTATAAAAGGACAGATAAAAAACGAATCCTGAACGGCTGCGGCAGGATGGACATCAAATAGAATGTCAGGa                                                                                                               >  7:183703/1‑149 (MQ=255)                                     gCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATtggct                                                                                                                      >  3:62901/1‑137 (MQ=255)                                     gCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATtggct                                                                                                                      <  4:62901/137‑1 (MQ=255)                                            cAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAg                                                                                                    >  5:229480/1‑148 (MQ=255)                                              gggCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGTCTGGCAGGAAGGTAAATaagaag                                                                                                 >  6:227174/1‑149 (MQ=255)                                                        cGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATg                                                                                        >  1:221427/1‑148 (MQ=255)                                                                     tGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCAGTAAAAGGAGAGATTTATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAATTTGGCTGGCAGGAAGGTACATTAGAAGGATTGCATGAACAAGCCATTaa                                                                           >  6:58735/1‑148 (MQ=37)                                                                       gCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAAt                                                                        >  2:70839/1‑149 (MQ=255)                                                                            aaCCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAAt                                                                                                       >  8:102928/1‑113 (MQ=255)                                                                            aaCCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAAt                                                                                                       <  7:102928/113‑1 (MQ=255)                                                                             aCCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCttt                                                                  <  6:229480/149‑1 (MQ=255)                                                                               ccAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTgc                                                                >  1:327853/1‑149 (MQ=255)                                                                               ccAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTgc                                                                >  7:309752/1‑149 (MQ=255)                                                                                    tCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCGGGAAGGTATATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATg                                                           >  2:124154/1‑149 (MQ=255)                                                                                    tCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATg                                                           >  2:177813/1‑149 (MQ=255)                                                                                        tGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTg                                                        >  8:345267/1‑148 (MQ=255)                                                                                                atatTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGTTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAgg                                                 <  8:55355/147‑1 (MQ=255)                                                                                                  atTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGa                                                                                                               >  4:168019/1‑83 (MQ=255)                                                                                                  atTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGa                                                                                                               <  3:168019/83‑1 (MQ=255)                                                                                                     ccGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTg                                           <  2:327853/148‑1 (MQ=255)                                                                                                      cGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGAt                                         >  1:139510/1‑149 (MQ=255)                                                                                                           tGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGa                                    >  6:34007/1‑149 (MQ=255)                                                                                                            cgccatAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGAc                                   <  4:131129/144‑1 (MQ=255)                                                                                                             tCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAAtt                                                                                                      <  5:388725/81‑1 (MQ=255)                                                                                                             tCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAAtt                                                                                                      >  6:388725/1‑81 (MQ=255)                                                                                                               aTTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAg                                <  1:70839/149‑1 (MQ=255)                                                                                                                ttAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAgg                               >  3:155137/1‑149 (MQ=255)                                                                                                                   aaaGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTg                             <  2:221427/148‑1 (MQ=255)                                                                                                                   aaaGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGc                            >  3:335212/1‑149 (MQ=255)                                                                                                                    aaGGAGAGATTAATGCCTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCt                           >  7:287720/1‑149 (MQ=255)                                                                                                                             ttAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCAc                  <  8:309752/149‑1 (MQ=255)                                                                                                                                     tATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTaa          >  4:147298/1‑149 (MQ=255)                                                                                                                                      aTTGCTGAACGGCTACGGCAGGAAGGGCATCAAATTGGCTGGCAGGAAGGTAAATTAGaa                                                                                                  >  4:371781/1‑60 (MQ=11)                                                                                                                                      aTTGCTGAACGGCTACGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGaa                                                                                                  <  3:371781/60‑1 (MQ=255)                                                                                                                                       ttGCTGAACGGCTGCGGCAGGAAGGACAACAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGAATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGc        >  5:219259/1‑149 (MQ=255)                                                                                                                                          cTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCAt                                                                              <  2:387582/76‑1 (MQ=255)                                                                                                                                          cTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCAt                                                                              >  1:387582/1‑76 (MQ=255)                                                                                                                                          cTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCg       >  5:236398/1‑147 (MQ=255)                                                                                                                                           tGAACGGCTACGGCAGGAAGGGCATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCa                                                                                          >  2:183886/1‑63 (MQ=255)                                                                                                                                           tGAACGGCTACGGCAGGAAGGGCATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCa                                                                                          <  1:183886/63‑1 (MQ=255)                                                                                                                                             aaCGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCTCGGCCACCCAGCTAAGCGAAGcc  >  8:285650/1‑149 (MQ=255)                                                                                                                                             aaCGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGc   <  4:335212/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                              TATGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGAGATTGTGCTGGCGACAACCCAACTCACTGATGCTGATATTCCGAACTGTCATTAAAAGGAGAGATTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTAAATTAGAAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCC  >  NC_000913/2357689‑2357977

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: ‑