Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 982,358 C→T 9.3% P438S (CCA→TCA)  ldtD → murein L,D‑transpeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913982,3580CT 9.3% 121.6 / 3.2 43P438S (CCA→TCA) ldtDmurein L,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base C (19/20);  new base T (2/2);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.47e-01

AGAACGGCAATCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTACCGTTCCGCTTCCAGCAGGCTC  >  NC_000913/982215‑982505
                                                                                                                                               |                                                                                                                                                   
aGAACGGCAATCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCaaaa                                                                                                                                                <  4:99578/149‑1 (MQ=255)
 gAACGGCAATCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAg                                                                                                                                               >  1:110876/1‑149 (MQ=255)
        aaTCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCaa                                                                                                                                        >  8:326/1‑149 (MQ=255)
         aTCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAAc                                                                                                                                       <  2:110876/149‑1 (MQ=255)
         aTCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCATTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAAc                                                                                                                                       >  3:50243/1‑149 (MQ=255)
             ggTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATc                                                                                                                                   <  3:174755/149‑1 (MQ=255)
                      ttCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAATGATATTCTGCCAAAAGTGCGCAACGATCCGGGATAtc                                                                                                                          <  6:58501/149‑1 (MQ=255)
                         gcgAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATAtctc                                                                                                                        >  7:106756/1‑148 (MQ=255)
                            aGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGa                                                                                                                      >  1:174381/1‑147 (MQ=255)
                                       gtcgCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCta                                                                                                          >  3:106066/1‑148 (MQ=255)
                                            cccGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCCACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATGCGGGATATCTCGAAAGCCATGGCTATACGGt                                                                                                    >  4:221164/1‑149 (MQ=255)
                                                   gCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATgcg                                                                                              <  4:106066/148‑1 (MQ=255)
                                                            cGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGaa                                                                                     >  1:210134/1‑148 (MQ=255)
                                                                 atgaGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAAcagca                                                                                <  2:174381/148‑1 (MQ=255)
                                                                    aGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCagag                                                                             <  3:135516/148‑1 (MQ=255)
                                                                         tGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGa                                                                       >  6:235264/1‑149 (MQ=255)
                                                                           cccTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTTGCACGCAAAGATATTCTGCAAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGAtt                                                                     <  8:22515/149‑1 (MQ=255)
                                                                           cccTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGAtt                                                                     <  3:69056/149‑1 (MQ=255)
                                                                           cccTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGAtt                                                                     <  8:106756/149‑1 (MQ=255)
                                                                                   aacGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATg                                                             >  1:188233/1‑149 (MQ=255)
                                                                                      gTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATgg                                                            >  1:42909/1‑147 (MQ=255)
                                                                                         gTGGGAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAg                                                                          >  2:162584/1‑130 (MQ=255)
                                                                                         gTGGCAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAg                                                                          <  1:162584/130‑1 (MQ=255)
                                                                                          tGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGtt                                                      <  6:167815/149‑1 (MQ=255)
                                                                                          tGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGAACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGtt                                                      <  6:121560/149‑1 (MQ=255)
                                                                                                 cccGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGt                                               >  8:121117/1‑149 (MQ=255)
                                                                                                    gccgTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTa                                            <  2:188233/149‑1 (MQ=255)
                                                                                                          gAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATc                                       <  4:103538/148‑1 (MQ=255)
                                                                                                              gTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTgg                                                                                       <  6:157074/96‑1 (MQ=255)
                                                                                                              gTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTgg                                                                                       >  5:157074/1‑96 (MQ=255)
                                                                                                                  cTCCAACTCTGGCACGCAAAGATATTCTGTCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCt                                >  8:61063/1‑147 (MQ=255)
                                                                                                                  cTCCAACTCTGGCACGCAAAGATATTCTGTCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCt                                <  7:64611/147‑1 (MQ=255)
                                                                                                                  cTCCAACTCTGGCACGCAAAGATATTCTGTCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCt                                <  7:61063/147‑1 (MQ=255)
                                                                                                                  cTCCAACTCTGGCACGCAAAGATATTCTGTCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCt                                >  8:64611/1‑147 (MQ=255)
                                                                                                                  cTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTc                               >  6:12618/1‑148 (MQ=255)
                                                                                                                   tCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCg                              >  6:90882/1‑148 (MQ=255)
                                                                                                                    ccAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCAc                                     >  3:192707/1‑140 (MQ=255)
                                                                                                                        ctctGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTa                        <  7:326/149‑1 (MQ=255)
                                                                                                                        ctctGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATAGCTCGAAATCCATGGCGATACGGAGATGCGCGGCTGGACCAGCAGAGCAGCGAGTGACCCATGGCAGGTGGACTGGTCTACAATCACGGCCTCGAATGTa                        >  2:72371/1‑149 (MQ=255)
                                                                                                                               aCGCAAAGATATTCTGCCAAAAGTGCTCAACGATCCGGGATATCTCGAAAGCCATTGCTATACGGTGATGCGCGGCTGGAACAGAAGAGAAGCGATTGAACCATGGCAGTTTGACTTGTCTACAATCACGGCCTCGAATTTACCGTTc                  <  6:183192/148‑1 (MQ=255)
                                                                                                                               aCGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTACCGTTcc                 <  7:121117/149‑1 (MQ=255)
                                                                                                                                          ttCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTACCGTTCCGCTTCcagcag      <  5:90882/149‑1 (MQ=255)
                                                                                                                                             tGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTACCGTTCCGCTTCCAGCAGGCt   >  1:112670/1‑149 (MQ=255)
                                                                                                                                               ccAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTACCGTTCCGCTTCCAGCAGGCTc  >  6:27421/1‑148 (MQ=255)
                                                                                                                                               |                                                                                                                                                   
AGAACGGCAATCAGGTGCTGGATTCGCGAGTCATTGTCGGTCGCCCCGATCGCAAAACGCCGATGATGAGCAGTGCCCTTAACAACGTAGTGGTAAACCCGCCGTGGAACGTACCTCCAACTCTGGCACGCAAAGATATTCTGCCAAAAGTGCGCAACGATCCGGGATATCTCGAAAGCCATGGCTATACGGTGATGCGCGGCTGGAACAGCAGAGAAGCGATTGACCCATGGCAGGTTGACTGGTCTACAATCACGGCCTCGAATTTACCGTTCCGCTTCCAGCAGGCTC  >  NC_000913/982215‑982505

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑