Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_pgi 4,185,645 G→C R99P (CGT→CCT)  rpoC → RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi4,185,6450GC96.1% 152.6 / NA 51R99P (CGT→CCT) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base C (26/23);  minor base T (0/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 2.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTGACGGCCTTTTCTGCGCCCGTATCTTTGGGCCGGTAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCGTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACTTTGAATCCTATG  >  NC_000913_3_pae_pgi/4185505‑4185782
                                                                                                                                            |                                                                                                                                         
acttcaCGGCCTTTTCTGCGCCCGTATCTTTGGGCCGGTAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTa                                                                                                                                   <  1:438078/144‑1 (MQ=255)
                tGCGCCCGTCTCTTTGGGCCGGTAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACt                                                                                                                   <  2:640282/149‑1 (MQ=255)
                  cgcCCGTATCTTTGGGCCGGTAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTgg                                                                                                                 <  1:859629/149‑1 (MQ=255)
                          tCTTTGGGCCGGTAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCg                                                                                                         >  1:197519/1‑149 (MQ=255)
                                      tAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATc                                                                                             >  1:865527/1‑149 (MQ=255)
                                      tAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCACCTCAAACACCGTGGCGTCGTCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGcacacc                                                                                             >  1:267390/1‑147 (MQ=255)
                                       aaaaGCTTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGACACAACGAGGCATCATGCGTGCGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGGCTGGGCCCCATCGAACTGGCTTCCCCGACTGCGCACAGCt                                                                                            >  2:811578/1‑149 (MQ=255)
                                            aTTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTc                                                                                       >  2:750704/1‑149 (MQ=255)
                                                 gAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGaa                                                                                  >  2:395237/1‑149 (MQ=255)
                                                 gAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGGAAGGAGTGCGGCTTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACCTCTGGTTCCTgca                                                                                  >  2:1106543/1‑147 (MQ=255)
                                                     ggcTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTCCGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCg                                                                              <  2:467150/147‑1 (MQ=255)
                                                       cTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCt                                                                            <  1:505989/149‑1 (MQ=255)
                                                             ggTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGAGCCAGACCTAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTc                                                                      >  1:538779/1‑149 (MQ=255)
                                                              gTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGGTGCCGTcc                                                                     >  2:411026/1‑149 (MQ=255)
                                                              gTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTcc                                                                     >  2:488900/1‑149 (MQ=255)
                                                               tAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTccc                                                                    >  2:240163/1‑149 (MQ=255)
                                                                      aaGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGtcgcgc                                                             >  2:793338/1‑144 (MQ=255)
                                                                         cgcCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTct                                                          >  1:726091/1‑149 (MQ=255)
                                                                           ccTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTctgc                                                        >  1:252205/1‑149 (MQ=255)
                                                                                tacacCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGGGGCCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTc                                                   <  2:1112378/148‑1 (MQ=255)
                                                                                 acacCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGACTGGGCCACATCGAACTCGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTCCCGTCCCGTATCGGTCTGCTGCTCg                                                  >  1:1093391/1‑149 (MQ=255)
                                                                                  cacCGTGGCGTCATCTGTGAGAAGGGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCTTGAGCGTATGGGCCACATCGAACTGGCGTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGa                                                 <  1:793338/149‑1 (MQ=255)
                                                                                    ccGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGata                                               <  1:130607/149‑1 (MQ=255)
                                                                                      gTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATg                                             >  1:52851/1‑149 (MQ=255)
                                                                                         gCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTccc                                                                    >  2:62574/1‑123 (MQ=255)
                                                                                         gCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTccc                                                                    <  1:62574/123‑1 (MQ=255)
                                                                                              aTCTGTGAGAAGTGGGGCGTTGAAATGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTgcg                                     >  1:1049593/1‑149 (MQ=255)
                                                                                              aTCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCATATCGGTCTGCTGCTCGTCATGCCGCTgcg                                     >  1:466809/1‑149 (MQ=255)
                                                                                               tCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTgcgc                                    <  2:252205/149‑1 (MQ=255)
                                                                                               tCTGTGAGAAGTGCGGCGTTGAACTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCTGACTGCGCGCATCTGCTTCCTGAAAGCGCTGCCGTCCCGTCTCGGTCTGCTGCTCGATATGCCGCTgcgc                                    <  1:1022335/149‑1 (MQ=255)
                                                                                                 agggagaGGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGa                                  <  2:910100/146‑1 (MQ=255)
                                                                                                   tgATAAGTGCGGCGTTGAAGTGACCCAGACTAACGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGTTATGCCGCTGCGCGata                                <  2:538779/149‑1 (MQ=255)
                                                                                                         gTGCGGCGTTGACGTGACACAGCCTAAAGTACGTCCTGCGAGACTGCGCTCTTTCGCTCTAGGGCCGCCTACTGTGAACCTTTGGTTCCGTAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAAc                          <  2:865527/149‑1 (MQ=255)
                                                                                                         gTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAAc                          >  1:141435/1‑149 (MQ=255)
                                                                                                          tGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTAt                                                                >  2:915744/1‑110 (MQ=255)
                                                                                                          tGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTAt                                                                <  1:915744/110‑1 (MQ=255)
                                                                                                           gcggcgTTTAAGGTCCCCAGACTAAAGTACGCCTTGGGCGTATTGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAActc                        <  2:267390/149‑3 (MQ=255)
                                                                                                              gcgTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCgta                     <  2:630618/149‑1 (MQ=255)
                                                                                                              gcgTTGAAGTGACCCAGACTAAAGGACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCgta                     <  2:535111/149‑1 (MQ=255)
                                                                                                               cgTTGAAGTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCgtac                    <  2:52851/149‑1 (MQ=255)
                                                                                                                      gTGACCCAGACTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACtt             <  2:828719/149‑1 (MQ=255)
                                                                                                                          cccAGACTAAAGTACGCCCGGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACTTTGaa         <  2:91589/149‑1 (MQ=255)
                                                                                                                           ccAGACTAAATTACGCCCGGAGCGGACGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACTTTGAAt        <  2:313249/149‑1 (MQ=255)
                                                                                                                               aCTAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTACCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACTTTGAATCCTa    >  1:1206956/1‑149 (MQ=255)
                                                                                                                                 tAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCgtac                    <  1:322826/131‑1 (MQ=255)
                                                                                                                                 tAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCgtac                    >  2:322826/1‑131 (MQ=255)
                                                                                                                                 tAAAGTACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACTTTGAATCTTAtg  >  1:265119/1‑149 (MQ=255)
                                                                                                                                      tACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGat                                                >  1:176849/1‑98 (MQ=255)
                                                                                                                                      tACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGat                                                <  2:176849/98‑1 (MQ=255)
                                                                                                                                      tACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTgcgc                                    >  2:651501/1‑110 (MQ=255)
                                                                                                                                      tACGCCCTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTgcgc                                    <  1:651501/110‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                         
ACGTGACGGCCTTTTCTGCGCCCGTATCTTTGGGCCGGTAAAAGATTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCGTGAGCGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCGATATCGAACGCGTACTGTACTTTGAATCCTATG  >  NC_000913_3_pae_pgi/4185505‑4185782

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑