Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,456,803 (C)6→5 coding (427/1953 nt) gspD → Type II secretion system protein GspD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,456,8030C.96.2% 105.7 / ‑2.1 26coding (427/1953 nt)gspDType II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (14/11);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.26e-01

TGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGATTCTTAATCAATTAATCAGCGAAAGCCACGGTAAAAGCCAGATGCCAGCCCTCCT  >  NC_000913/3456577‑3457053
                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                          
tGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCggg                                                                                                                                                                                                                                   >  1:199091/1‑251 (MQ=255)
               aCAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGTTAGCGTCGGTAAtgt                                                                                                                                                                                                                    <  2:327337/251‑1 (MQ=255)
                       actacCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGCGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCAtt                                                                                                                                                                                                            <  2:302460/251‑1 (MQ=255)
                          acCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAATTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGCTGCGGGTAGCGTCGGTAATGTTGTGCATTATg                                                                                                                                                                                                         >  2:54065/1‑251 (MQ=255)
                                tCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCt                                                                                                                                                                                                   >  2:375529/1‑251 (MQ=255)
                                      tAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAAc                                                                                                                                                                                              <  1:211538/250‑1 (MQ=255)
                                             tCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTAt                                                                                                                                                                                      >  1:336789/1‑251 (MQ=255)
                                               ttGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTc                                                                                                                                                                                    >  2:37131/1‑251 (MQ=255)
                                                tGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGCTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGAGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCt                                                                                                                                                                                   >  1:47183/1‑251 (MQ=255)
                                                         cGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCg                                                                                                                                                                          <  2:329049/251‑1 (MQ=255)
                                                                   gTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccacc                                                                                                                                                                >  1:311032/1‑251 (MQ=255)
                                                                          cGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATtaat                                                                                                                                                          >  1:262324/1‑250 (MQ=255)
                                                                                    tGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGGAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                                                                                                                >  1:158080/1‑250 (MQ=255)
                                                                                                            aGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCAt                                                                                                                       >  1:71386/1‑251 (MQ=255)
                                                                                                               tAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                                                                                                                    >  1:229044/1‑251 (MQ=255)
                                                                                                                aaTGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                                                                                                                    <  1:37131/250‑1 (MQ=255)
                                                                                                                 aTGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGCACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTTTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGc                                                                                                                   >  2:192087/1‑251 (MQ=255)
                                                                                                                 aTGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGAAGGTGAAGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTATTATTCTGACCGGTCGTGCCTCAACCATTAATAAACTGATTGAAGACATAAAGCGCGTTGATGTCATCGGc                                                                                                                   >  1:30590/1‑250 (MQ=255)
                                                                                                                                    gatgatTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAattat                                                                                               <  1:131031/251‑1 (MQ=255)
                                                                                                                                     atgatTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAattatt                                                                                              >  1:107484/1‑251 (MQ=255)
                                                                                                                                                       cGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAAAAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGt                                                                              <  1:208039/249‑1 (MQ=255)
                                                                                                                                                               cGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGa                                                                    <  2:411/251‑1 (MQ=255)
                                                                                                                                                                           gTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGAt                                                        <  2:125670/251‑1 (MQ=255)
                                                                                                                                                                                   cccGAATTGTACCGCTTGATAACGTTCCTGCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGTTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGATTCTTAATc                                                <  1:225070/251‑1 (MQ=255)
                                                                                                                                                                                                                gCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGATTCTTAATCAATTAATCAGCGAAAGCCACGGTAAAAg                    <  2:47183/250‑1 (MQ=255)
                                                                                                                                                                                                                gCTCGTGACCTGGCCCCC‑TGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGATTCTTAATCAATTAATCAGCGAAAGCCACGGTAAAAGc                   >  1:114502/1‑251 (MQ=255)
                                                                                                                                                                                                                                  cTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGATTCTTAATCAATTAATCAGCGAAAGCCACGGTAAAAGCCAGATGCCAGCcctcct  >  2:57037/1‑251 (MQ=255)
                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                          
TGATACGTTTAGCCAACAGGAGTACTACCAGTTCTTTTTAAGTATTCTTGATCTTTACGGTTATTCCGTGATCACGCTGGACAATGGTTTTCTGAAAGTGGTTCGCTCAGCTAATGTAAAAACATCGCCAGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATATGCGTCAGCGGAAGATCTCGCCGAGATTCTTAATCAATTAATCAGCGAAAGCCACGGTAAAAGCCAGATGCCAGCCCTCCT  >  NC_000913/3456577‑3457053

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑