Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091375,0790CT42.5% 47.3 / 27.2 40L134L (CTG→CTA) thiBthiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base C (3/20);  new base T (17/0);  total (20/20)
Fisher's exact test for biased strand distribution p-value = 2.57e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGT  >  NC_000913/74931‑75227
                                                                                                                                                    |                                                                                                                                                    
gCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCa                                                                                                                                                     <  2:683302/150‑1 (MQ=255)
           ggggCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGt                                                                                                                                         <  1:309480/151‑1 (MQ=255)
               cGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTtttttttat                                                                                                                                      >  1:522030/1‑145 (MQ=255)
               cGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTTTTTGTCAt                                                                                                                                      >  2:29900/1‑150 (MQ=255)
                gTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGttttgttttgt                                                                                                                                         >  1:530123/1‑138 (MQ=255)
                 tCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTTTTTTTGTTATaa                                                                                                                                    >  2:561519/1‑150 (MQ=255)
                        cATAGACTTTTTGCACCCATAGCAACAGCCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAACCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAg                                                                                                                              <  1:363857/149‑1 (MQ=255)
                           agctttgtcgCACCCATAGCAACGGGCCCACCCCCGGTGTCCTGGTGCCCGGTTCCTGAAAAATCCCCCGCCAGTTTTGATCGCCCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGc                                                                                                                            <  1:608739/139‑1 (MQ=255)
                                    gCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTCTTTTTTTCATAAACTAAGGCGAAGTAgacct                                                                                                                 >  2:211994/1‑146 (MQ=255)
                                    gCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATa                                                                                                                <  2:108565/151‑1 (MQ=255)
                                      aTCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAAt                                                                                                              <  2:42938/151‑1 (MQ=255)
                                              cAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTCGTTTGTTTTTTTCTTAAAAAAAGACGAGAGAGCGATAATCaaa                                                                                                          >  1:147749/1‑147 (MQ=255)
                                               aaCACACCCAGCCCCGGTGTACTGGGGCGCGGGTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAAc                                                                                                         <  1:59396/147‑1 (MQ=255)
                                                  aGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTCTTTTTATAAAAAAAAGCGGAGGAAGCCTAATCAAAAAGTACg                                                                                                   >  2:453620/1‑150 (MQ=255)
                                                      ccAGCCCCGGTGTCCTGGTGCGCGGACCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAgt                                                                                              <  2:33430/151‑1 (MQ=255)
                                                      ccAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTTTTCTTGTAATCAAAAAAGGGGAAGAAGCAATAATAAAACGGAACGaaaat                                                                                              >  2:154164/1‑149 (MQ=255)
                                                      ccAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAgt                                                                                              <  2:83136/151‑1 (MQ=255)
                                                       cAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTCGTTTTTTTTTTTTTTAAAAACAAGGGAAGGAGCCCTAATAAAAAAGGACGaaa                                                                                                >  2:243862/1‑148 (MQ=255)
                                                              ggTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTTTTTTTTTTATAAACAAAGGCGAAGTAGCCATAATCAAAAGGTACGAAAGGGGtattat                                                                                      >  1:280329/1‑151 (MQ=255)
                                                              ggTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCattat                                                                                      <  1:668161/151‑1 (MQ=255)
                                                               gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCattatt                                                                                     <  2:643258/151‑1 (MQ=255)
                                                                 gtACTGGTGCGCGGATCCTGAAAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTc                                                                                    <  1:263299/150‑1 (MQ=255)
                                                                         gcgcGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGccgccg                                                                           <  2:682033/151‑1 (MQ=255)
                                                                             ggATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTCTTTTTTCTTTTTATAAAAGAAGACGAAGTAGGCCTAAATAAAAAGGACAAAAGTGGTTTTATTCCAcccgcc                                                                            >  2:402937/1‑146 (MQ=255)
                                                                                  cTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTTTCTTAAAAGAAGGCGGAGTAGGCATAATCAAAAGGGACGAAAGGGGTATTTTTTTAGCCGCCcggggcgt                                                                    >  1:641118/1‑144 (MQ=255)
                                                                                       aaaTCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACgg                                                              <  1:478483/150‑1 (MQ=255)
                                                                                             cccGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTTTTTTTTATAAAAAAAAGCGAAGGAGCCATAATTAAAAAGGAAGAAAGAGGCATTATTTCAGCCCCCGGGGACGGTAAAGGCATCCGc                                                       >  2:269666/1‑151 (MQ=255)
                                                                                                gCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGc                                                    <  2:27231/151‑1 (MQ=255)
                                                                                                 ccAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGGTTGTTCTTTTTATTAAAGAAGGCGAAGGAGCCCTAAACAAAAAGTACGAAAATGTCATTATTTCACCCGCCGGGGACGGTAACGGCAACCGccccc                                                   >  1:423233/1‑147 (MQ=255)
                                                                                                                ctcAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTgg                                      <  1:686279/149‑1 (MQ=255)
                                                                                                                   aaCCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCaaa                                  <  1:225147/150‑1 (MQ=255)
                                                                                                                     ccAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTGTCTTAAACGAAGGCGGAGTAGGCATAATCAAACGGTACGAAAGTGTTATTTTTTCACCCGCCGGGGACGGTAAAGGCATCCGCCGCCACACCCCTTTTTGCAAACa                                >  1:217068/1‑150 (MQ=255)
                                                                                                                     ccAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTGTTGTAAAACAAAGGGGAGGAGCCGCAAAAAAAACGGACGAAAAGGTCCTTATTTCAGCCGCCGGGGAGGGTTACCGGATACGCCGCCCCAccccccttttccaaca                                >  2:588364/1‑136 (MQ=255)
                                                                                                                      cAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGt                              <  2:280835/151‑1 (MQ=255)
                                                                                                                      cAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTCATAAAAAAAGGCGGAGGAGGCATAATCAAAAGGGACGAAAGAGTCATTTTTTCAGCCGCCGGGGACGGTAACGGCCTCCCCCGCCCCCCCCCCTTTTGCAAACa                                >  2:507490/1‑149 (MQ=255)
                                                                                                                                aGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTAc                    <  2:251945/151‑1 (MQ=255)
                                                                                                                                       gtgGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCGTCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTggcggc             <  1:414433/151‑1 (MQ=255)
                                                                                                                                              gTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAAc      >  2:660132/1‑151 (MQ=255)
                                                                                                                                                 tttCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAgg   >  1:301125/1‑151 (MQ=255)
                                                                                                                                                  ttCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGgt  >  2:341494/1‑151 (MQ=255)
                                                                                                                                                    |                                                                                                                                                    
GCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGT  >  NC_000913/74931‑75227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑