Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,945,985 C→T 9.4% intergenic (‑143/+96) tcdA ← / ← mltA tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,945,9850CT 9.4% 164.8 / 5.5 53intergenic (‑143/+96)tcdA/mltAtRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
Reads supporting (aligned to +/- strand):  ref base C (24/24);  new base T (2/3);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

CCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCACC  >  NC_000913/2945881‑2946126
                                                                                                        |                                                                                                                                             
ccTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    <  3:69235/148‑1 (MQ=255)
                              cTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAgg                                                                                                         >  2:883618/1‑113 (MQ=255)
                              cTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAgg                                                                                                         <  1:883618/113‑1 (MQ=255)
                                tATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACgcgc                                                                                                                           >  2:994246/1‑93 (MQ=255)
                                tATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACgcgc                                                                                                                           <  1:994246/93‑1 (MQ=255)
                                tATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCaataat                                                                                                             >  4:287037/1‑107 (MQ=255)
                                tATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCaataat                                                                                                             <  3:287037/107‑1 (MQ=255)
                                  tCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATGCGGCGTGAACGCCTTATCCgg                                                                                                                                         >  1:369477/1‑77 (MQ=25)
                                  tCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATGCGGCGTGAACGCCTTATCCgg                                                                                                                                         <  2:369477/77‑1 (MQ=25)
                                  tCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTc                                                                                        >  4:207882/1‑126 (MQ=255)
                                  tCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTc                                                                                        <  3:207882/126‑1 (MQ=255)
                                   cAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    <  1:298033/113‑1 (MQ=255)
                                   cAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    >  2:298033/1‑113 (MQ=255)
                                   cAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTAcc                                                                                            <  4:761174/121‑1 (MQ=255)
                                   cAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTAcc                                                                                            >  3:761174/1‑121 (MQ=255)
                                                  ccTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCGGGAtgtg                                                                                                    <  4:95006/98‑1 (MQ=255)
                                                  ccTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    >  4:29168/1‑98 (MQ=255)
                                                  ccTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    <  3:29168/98‑1 (MQ=255)
                                                  ccTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGACGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    >  3:95006/1‑98 (MQ=255)
                                                     gCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATc                                                   >  2:334521/1‑144 (MQ=255)
                                                     gCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATc                                                   <  1:334521/144‑1 (MQ=255)
                                                            tttGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTAcc                                                                                            <  2:482554/96‑1 (MQ=255)
                                                            tttGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTAcc                                                                                            >  1:482554/1‑96 (MQ=255)
                                                            tttGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTaaaaa                                                                   <  4:233695/121‑1 (MQ=255)
                                                            tttGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTaaaaa                                                                   >  3:233695/1‑121 (MQ=255)
                                                                  tttGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGt                                                                                 <  1:733134/101‑1 (MQ=255)
                                                                  tttGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGt                                                                                 >  2:733134/1‑101 (MQ=255)
                                                                    tGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATa                                                            <  2:104420/120‑1 (MQ=255)
                                                                    tGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATa                                                            >  1:104420/1‑120 (MQ=255)
                                                                       aTGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGa                                                                                                   <  2:38016/78‑1 (MQ=255)
                                                                       aTGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGa                                                                                                   >  1:38016/1‑78 (MQ=255)
                                                                        tGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACACCGCGCACTTAGTCAATAATCAGGATGTGAGGTTAc                                                                                             >  4:325706/1‑83 (MQ=255)
                                                                        tGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACACCGCGCACTTAGTCAATAATCAGGATGTGAGGTTAc                                                                                             <  3:325706/83‑1 (MQ=255)
                                                                        tGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTa                                                                                              <  1:915242/82‑1 (MQ=255)
                                                                        tGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTa                                                                                              >  2:915242/1‑82 (MQ=255)
                                                                          aTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATc                                                   <  1:662348/123‑1 (MQ=255)
                                                                          aTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATc                                                   >  2:662348/1‑123 (MQ=255)
                                                                                   ccGGATGCGGCGTGAACGCCTTATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTg                                                                                  >  4:686740/1‑83 (MQ=21)
                                                                                   ccGGATGCGGCGTGAACGCCTTATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTg                                                                                  <  3:686740/83‑1 (MQ=21)
                                                                                   ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCt                                                                                         <  4:1054194/76‑1 (MQ=255)
                                                                                   ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCt                                                                                         >  3:1054194/1‑76 (MQ=255)
                                                                                   ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGt                                                                                 >  2:43363/1‑84 (MQ=255)
                                                                                   ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGt                                                                                 <  1:43363/84‑1 (MQ=255)
                                                                                     ggatgcggCGTGAACGCCTTATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGtt                              <  2:1056028/127‑1 (MQ=39)
                                                                                        tAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTaaaaa                                                                   <  1:610918/93‑1 (MQ=255)
                                                                                        tAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTaaaaa                                                                   >  2:610918/1‑93 (MQ=255)
                                                                                        tAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGt            >  3:1070545/1‑148 (MQ=255)
                                                                                         aaGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGtt           >  1:548851/1‑148 (MQ=255)
                                                                                          aGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTAcc                           <  4:261578/131‑1 (MQ=255)
                                                                                          aGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTAcc                           >  3:261578/1‑131 (MQ=255)
                                                                                            gCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    <  4:1084045/56‑1 (MQ=255)
                                                                                            gCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGAtgtg                                                                                                    >  3:1084045/1‑56 (MQ=255)
                                                                                                  aCGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCAcc  <  4:1070545/148‑1 (MQ=255)
                                                                                                   cgccgcATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCAcc                                                                                     <  3:815042/64‑1 (MQ=255)
                                                                                                   cgccgcATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCAcc                                                                                     >  4:815042/1‑64 (MQ=255)
                                                                                                        |                                                                                                                                             
CCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCACC  >  NC_000913/2945881‑2946126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: