Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,412,000 C→T *412* (TAG→TAA)  intR ← Rac prophage, integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,412,0000CT96.7% 186.7 / ‑1.1 60coding (1236/1236 nt)intRRac prophage, integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (29/29);  minor base . (1/1);  total (30/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

GCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGC  >  NC_000913/1411868‑1412134
                                                                                                                                    |                                                                                                                                      
gCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGAt                                                                                                                                  >  1:551150/1‑139 (MQ=255)
                aGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACa                                                                                                                  <  2:645312/139‑1 (MQ=255)
                  aCGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATg                                                                                                                >  1:1016388/1‑139 (MQ=255)
                      ttttGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTa                                                                                                            <  2:751488/139‑1 (MQ=255)
                             aTTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtc                                                                                                     <  2:551150/139‑1 (MQ=255)
                              tttGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcg                                                                                                    >  2:496513/1‑139 (MQ=255)
                                 gTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcgtcg                                                                                                 >  1:773455/1‑139 (MQ=255)
                                          gTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                        <  2:773455/139‑1 (MQ=255)
                                            aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                      <  2:740739/139‑1 (MQ=255)
                                            aTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                      >  1:929876/1‑139 (MQ=255)
                                                 tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                                                             >  2:992499/1‑95 (MQ=255)
                                                 tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACcg                                                                                                                             <  1:992499/95‑1 (MQ=255)
                                                  ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                   <  1:976413/104‑1 (MQ=255)
                                                  ctttctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                   >  2:976413/1‑104 (MQ=255)
                                                     tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                                         <  1:4528/95‑1 (MQ=255)
                                                     tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                                         >  2:4528/1‑95 (MQ=255)
                                                     tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                   <  1:1218148/101‑1 (MQ=255)
                                                     tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAAc                                                                                                                   >  2:1218148/1‑101 (MQ=255)
                                                     tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACAt                                                                             >  1:412676/1‑139 (MQ=255)
                                                     tctttGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACAt                                                                             >  2:1272015/1‑139 (MQ=255)
                                                          gTAATTTGTTGATTTTTTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATATCGt                                                                        <  2:929876/139‑1 (MQ=255)
                                                          gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCaa                                                                                    <  2:877238/127‑1 (MQ=255)
                                                          gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCaa                                                                                    >  1:877238/1‑127 (MQ=255)
                                                          gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGt                                                                        <  2:412676/139‑1 (MQ=255)
                                                          gTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGt                                                                        >  2:28025/1‑139 (MQ=255)
                                                                     aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGa                                                                                                                                   <  2:721199/69‑1 (MQ=255)
                                                                     aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGa                                                                                                                                   >  1:721199/1‑69 (MQ=255)
                                                                                ttattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgcgc                                                  <  1:1272015/139‑1 (MQ=255)
                                                                                 tattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCa                                                         >  2:1153727/1‑131 (MQ=255)
                                                                                 tattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCa                                                         <  1:1153727/131‑1 (MQ=255)
                                                                                   tttCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAA‑TACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                      >  1:957635/1‑99 (MQ=255)
                                                                                   tttCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAA‑TACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                      <  2:957635/99‑1 (MQ=255)
                                                                                             cttgTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATTGCTATCTGTtcg                                                                                                    <  1:731212/73‑1 (MQ=255)
                                                                                             ctGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcg                                                                                                    >  2:731212/1‑76 (MQ=255)
                                                                                              tGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGtt                                                                                                      <  1:647793/73‑1 (MQ=255)
                                                                                              tGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGtt                                                                                                      >  2:647793/1‑73 (MQ=255)
                                                                                                   cTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                               <  1:978828/139‑1 (MQ=255)
                                                                                                   cTAAATGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTtgg                               >  1:111183/1‑139 (MQ=255)
                                                                                                      aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                      <  1:495301/81‑1 (MQ=255)
                                                                                                      aaTGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcatc                                                                                      >  2:495301/1‑81 (MQ=255)
                                                                                                        tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATa                                                                                                                                 >  2:777282/1‑36 (MQ=255)
                                                                                                        tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATa                                                                                                                                 <  1:777282/36‑1 (MQ=255)
                                                                                                        tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                                         >  2:389606/1‑44 (MQ=255)
                                                                                                        tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCa                                                                                                                         <  1:389606/44‑1 (MQ=255)
                                                                                                        tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGtt                                                                                               >  1:576169/1‑70 (MQ=255)
                                                                                                        tGGGGCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGtt                                                                                               <  2:576169/70‑1 (MQ=255)
                                                                                                          gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcgtcg                                                                                                 <  2:478871/66‑1 (MQ=255)
                                                                                                          gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTtcgtcg                                                                                                 >  1:478871/1‑66 (MQ=255)
                                                                                                          gggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCta                        >  1:394/1‑139 (MQ=255)
                                                                                                           ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                        >  2:1104082/1‑74 (MQ=255)
                                                                                                           ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                        <  1:1104082/74‑1 (MQ=255)
                                                                                                           ggCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtat                       >  1:1052511/1‑139 (MQ=255)
                                                                                                            gCAAATTGGGGGCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtata                      <  2:394/139‑1 (MQ=255)
                                                                                                                     gggCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAAttt                                                                  <  2:612355/86‑1 (MQ=255)
                                                                                                                     gggCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAAttt                                                                  >  1:612355/1‑86 (MQ=255)
                                                                                                                      ggCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCcaca                                                                              <  2:272541/73‑1 (MQ=255)
                                                                                                                      ggCAAACTTTGCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCcaca                                                                              >  1:272541/1‑73 (MQ=255)
                                                                                                                                gCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                        <  2:1095490/53‑1 (MQ=255)
                                                                                                                                gCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtca                                                                                        >  1:1095490/1‑53 (MQ=255)
                                                                                                                                gCAATTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGc  <  1:496513/139‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                      
GCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGC  >  NC_000913/1411868‑1412134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑