Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,632,369 T→C intergenic (‑84/‑703) ydfJ ← / → ydfK pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,632,3690TC97.8% 167.8 / NA 46intergenic (‑84/‑703)ydfJ/ydfKpseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (25/20);  minor base A (1/0);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCG  >  NC_000913/1632221‑1632514
                                                                                                                                                    |                                                                                                                                                 
gatTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCAccc                                                                                                                                                 >  2:666575/1‑151 (MQ=255)
gatTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCAccc                                                                                                                                                 >  1:187825/1‑151 (MQ=255)
 atTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCt                                                                                                                                                >  2:324649/1‑151 (MQ=255)
     aGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGt                                                                                                                                            <  1:164064/151‑1 (MQ=255)
       gAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTc                                                                                                                                          <  1:132105/151‑1 (MQ=255)
        aaaaaaTATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCg                                                                                                                                         >  2:555932/1‑151 (MQ=255)
           aaaTATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGAtc                                                                                                                                      >  1:469842/1‑151 (MQ=255)
            aaTATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGAtct                                                                                                                                     >  2:74719/1‑151 (MQ=255)
                 ttCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAgtg                                                                                                                                >  2:373373/1‑151 (MQ=255)
                        aaCACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCt                                                                                                                         >  1:182575/1‑151 (MQ=255)
                         acacTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTg                                                                                                                        >  2:484007/1‑151 (MQ=255)
                           acTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTACTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTggg                                                                                                                      >  2:507947/1‑151 (MQ=255)
                              aaCGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTgggg                                                                                                                     <  1:71825/149‑1 (MQ=255)
                                   tGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGGGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTAttt                                                                                                              >  2:145434/1‑151 (MQ=255)
                                         gAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTcc                                                                                                        >  2:585885/1‑151 (MQ=255)
                                              aaTATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCata                                                                                                    <  2:664510/150‑1 (MQ=255)
                                                 ataACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATg                                                                                                >  1:631617/1‑151 (MQ=255)
                                                  taACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGc                                                                                               >  1:512755/1‑151 (MQ=255)
                                                    aCTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGccc                                                                                             >  2:186172/1‑151 (MQ=255)
                                                    aCTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGccc                                                                                             >  2:503332/1‑151 (MQ=255)
                                                       ggAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCa                                                                                           <  2:808651/150‑1 (MQ=255)
                                                        gAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCaa                                                                                          >  1:840107/1‑150 (MQ=255)
                                                         aaaTCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCaaaa                                                                                        <  2:512791/151‑1 (MQ=255)
                                                                 aaTTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTcc                                                                                 <  1:155486/150‑1 (MQ=255)
                                                                      acaGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACa                                                                           <  1:684809/151‑1 (MQ=255)
                                                                       caGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAg                                                                          <  1:504929/151‑1 (MQ=255)
                                                                          gtgtTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGAt                                                                        <  1:223404/150‑1 (MQ=255)
                                                                                 ttCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGtt                                                                >  1:633217/1‑151 (MQ=255)
                                                                                   cccATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGttt                                                               <  2:299032/150‑1 (MQ=255)
                                                                                          tgtgGTTTCCTAGGCGTTTTCTAGGTTTTTTCAGATAGTTGGATTTTTTTAAAAAGCAACCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTATGTCCACGATATTCCCCTAAAAAACTCCCCAACAGTTAAGTAGTTTTTTCATgg                                                       >  1:728627/1‑151 (MQ=255)
                                                                                           gtgGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATg                                                        <  1:389500/149‑1 (MQ=255)
                                                                                                 tCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTAt                                                 <  2:519866/150‑1 (MQ=255)
                                                                                                     tGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGt                                             >  2:498384/1‑150 (MQ=255)
                                                                                                      ggCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTaa                                           <  1:471866/151‑1 (MQ=255)
                                                                                                                  gTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACgg                               >  1:536686/1‑151 (MQ=255)
                                                                                                                    tttttCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCt                             >  1:188340/1‑151 (MQ=255)
                                                                                                                      tttCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTgg                           >  1:823630/1‑151 (MQ=255)
                                                                                                                       ttCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTgg                           >  2:203321/1‑150 (MQ=255)
                                                                                                                         cAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGaaa                        <  1:483971/151‑1 (MQ=255)
                                                                                                                            aTAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCa                     <  2:636350/151‑1 (MQ=255)
                                                                                                                              aGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCAt                    <  1:162513/150‑1 (MQ=255)
                                                                                                                                  gCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAAt               >  2:66705/1‑151 (MQ=255)
                                                                                                                                   cATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATa              <  1:566126/151‑1 (MQ=255)
                                                                                                                                     tttttttAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACt            >  2:165720/1‑151 (MQ=255)
                                                                                                                                      ttttttAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCACATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTc           >  2:144801/1‑151 (MQ=255)
                                                                                                                                           tAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCacac       <  2:840165/150‑1 (MQ=255)
                                                                                                                                            aaaaaGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACt      >  2:39422/1‑150 (MQ=255)
                                                                                                                                               aaGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCg  <  1:392244/151‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                 
GATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACTATCG  >  NC_000913/1632221‑1632514

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑