Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 3,370,347 G→A 9.7% Q145* (CAG→TAG)  sspA ← stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,370,3470GA 9.7% 115.0 / 3.9 42Q145* (CAG→TAG) sspAstringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog
Reads supporting (aligned to +/- strand):  ref base G (19/17);  new base A (2/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.11e-01

CCACTCATAGAATGCACGCAGCAGATAGGGACGACGTGGTGTTAGCTGTGACAAATCCATACAGATTAACTCCGGCCCAGACGCATTTCACGTTCTGCTTCAGTTAAAGAAGCAAGGAAAGAGTCACGCTCAAAGACGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACG  >  CP009273/3370076‑3370606
                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                   
ccACTCATAGAATGCACGCAGCAGATAGGGAAGACGTGGTGTTAGCTGTGACAAATCCATACAGATTAACTCCGGCCCAGACGCATTTCNCGTTCTGCTTCAGTTAAAGTAGCAAGGAAAGAGTCACGCTCAAAGACGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGa                                                                                                                                                                                                                                                                    <  1:514158/273‑1 (MQ=255)
                                                                aTTAACTCCGGGCCAGACGCATTTCACGTTCTGCTTCCGTTAAAGAAGCACGGAAAGAGTCACGCTCAAAGACGCGTGTCATATAGCCTTTCATCTCTTTCGCACCAGGCCCGCTGAACTCGATTCCCTGTTACGCCAGACGCCACAGCACCGGAGCAACATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTTACCAAAGCACGGCGCAATCGACAGCAGTTCATCGCGCAGTCGCTTCCGTGCGGCGTCTCCTTccaga                                                                                                                                                                                                  >  2:211422/1‑271 (MQ=255)
                                                                               gACGCATTTCACGTTCTGCTTCAGTTAAAGAAGAAAGGAAAGAGTCACGCTCAAAGACGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCAGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGtt                                                                                                                                                                                       <  1:211426/271‑1 (MQ=255)
                                                                                    aTTTCACGTTCTGCTTCAGTTAAAGAAGCTAGGAAAGAGTCACGCTCAAAGACGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCACCGGAGCAAGATAGCAATCGACCAGGCTGAACTCCTCGCTCAGGAAGTACGGCNTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACTTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGgt                                                                                                                                                                              >  1:458807/1‑275 (MQ=255)
                                                                                                                                   aaaGACGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGAcc                                                                                                                                                                                                                                                           >  2:305230/1‑151 (MQ=255)
                                                                                                                                       aCGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGgcg                                                                                                                                                                                                                                                       <  1:305235/151‑1 (MQ=255)
                                                                                                                                           gggTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGgcgc                                                                                                                                                                                                                                                      >  2:638351/1‑148 (MQ=255)
                                                                                                                                               cATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGATCGGCGCAATc                                                                                                                                                                                                                                                  <  1:638362/148‑1 (MQ=255)
                                                                                                                                                                             gCCGCTGAACTCGATGCCCAGTTGCGACAGACGCGACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTAACCGAAGAcc                                                                                                                                                                                                                                                           >  1:444439/1‑109 (MQ=255)
                                                                                                                                                                             ccggCTGAGCTCGCTGCTCAGTTGCGGCAGACGCCAGACCTGCGTAGAAAGATAGCAATGCACCCGGCTGAACTCATCGCACAGCAAGTACGGCTTCTGACCGAAGACCGGCGCCATCGCCAGCAGTTCTTCGCGCAGATGCTTACGTGCGGCATCCGCCGCAGAAGCGTAACCGTTGATGGTGGTGTTGATCCGCGTGTCCCAGTCTTTTTCGAGGCGGTGCATGTTCAGACAGCTGTGCCCGGGAGCCACCGGGGACGCGGGAATCAGTgcg                                                                                      >  2:99511/4‑272 (MQ=255)
                                                                                                                                                                                 cTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTAACCGAAGACCGgcg                                                                                                                                                                                                                                                       <  2:444433/109‑1 (MQ=255)
                                                                                                                                                                                                       gCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCcagcag                                                                                                                                                                                                                                          >  2:231875/1‑100 (MQ=255)
                                                                                                                                                                                                       gCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTtg                                                                                                                                                                                      >  1:157511/1‑152 (MQ=255)
                                                                                                                                                                                                           aCGCCACAGCAGCGGAGCAAGATAGCACTCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTtgatga                                                                                                                                                                                  <  2:157508/152‑1 (MQ=255)
                                                                                                                                                                                                           aCGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGttct                                                                                                                                                                                                                                      <  1:231879/100‑1 (MQ=255)
                                                                                                                                                                                                                       cGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCa                                                                                                                                                                                                                               >  2:630243/1‑95 (MQ=255)
                                                                                                                                                                                                                       cGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTg                                                                                                                                                                                              >  2:108155/1‑128 (MQ=255)
                                                                                                                                                                                                                         gAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTg                                                                                                                                                                                                          >  1:68820/1‑114 (MQ=255)
                                                                                                                                                                                                                           gCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGGTTCTTACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTg                                                                                                                                                                                                                           <  1:630254/95‑1 (MQ=255)
                                                                                                                                                                                                                           gCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAAcc                                                                                                                                                                                          <  1:108156/128‑1 (MQ=255)
                                                                                                                                                                                                                            cAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGttcttc                                                                                                                                                                                                                                    >  1:238757/1‑85 (MQ=255)
                                                                                                                                                                                                                             aaGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTc                                                                                                                                                                                                      <  2:68820/114‑1 (MQ=255)
                                                                                                                                                                                                                              aGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTtg                                                                                                                                                                                      >  1:26932/1‑129 (MQ=255)
                                                                                                                                                                                                                                aTAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCgcgc                                                                                                                                                                                                                                <  2:238753/85‑1 (MQ=255)
                                                                                                                                                                                                                                  aGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTtgatga                                                                                                                                                                                  <  2:26932/129‑1 (MQ=255)
                                                                                                                                                                                                                                    cAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGttcttc                                                                                                                                                                                                                                    >  1:312290/1‑77 (MQ=255)
                                                                                                                                                                                                                                        cGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCgcgc                                                                                                                                                                                                                                <  2:312285/77‑1 (MQ=255)
                                                                                                                                                                                                                                         gACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTAACCGAAGACCGGCGCAATCGCCAGCAGttcttc                                                                                                                                                                                                                                    >  1:297127/1‑72 (MQ=255)
                                                                                                                                                                                                                                          aCCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGa                                                              >  2:109029/1‑237 (MQ=255)
                                                                                                                                                                                                                                            cAGGCTGCACTCATCGCTCAGTAAGTACGGCGTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTACCACAGGGTCAGCTCAc                      <  1:99511/275‑1 (MQ=255)
                                                                                                                                                                                                                                             aGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTAACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCgcgc                                                                                                                                                                                                                                <  2:297122/72‑1 (MQ=255)
                                                                                                                                                                                                                                              ggCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATAtt                                                          <  1:109030/237‑1 (MQ=255)
                                                                                                                                                                                                                                                   aaCTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTtcat                                                                                                                                                                        >  2:48546/1‑122 (MQ=255)
                                                                                                                                                                                                                                                       cATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGc                                                                                                                                                                    <  1:48546/122‑1 (MQ=255)
                                                                                                                                                                                                                                                        aTCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGttcttc                                                                                                                                                                                                                                    >  1:275206/1‑57 (MQ=255)
                                                                                                                                                                                                                                                        aTCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGc                                                                                                                                                                                                >  1:211504/1‑93 (MQ=255)
                                                                                                                                                                                                                                                         tCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCCCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGCGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCCCCGCAACCTACCGGGTAAACAGGCATCAGCGCCGGATGCGGGAAACGCTCATCAAGATATTCCATAATGATGCGAGATTCCCACATGGTCAGCTCACGATctgccaatt          >  1:335644/1‑266 (MQ=255)
                                                                                                                                                                                                                                                            cTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCgcgc                                                                                                                                                                                                                                <  2:275201/57‑1 (MQ=255)
                                                                                                                                                                                                                                                            cTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGaa                                                                                                                                                                                            <  2:211500/93‑1 (MQ=255)
                                                                                                                                                                                                                                                                ggAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCCCATCCAGATATTCCATAAGAATGCGAGATTCCCACAGGGACAGCCCACGAACCACCAGGGTCGTAACg  >  2:564222/1‑275 (MQ=255)
                                                                                                                                                                                                                                                                       cgccTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTtgat                                                                                                                                                                                    >  2:417945/4‑90 (MQ=255)
                                                                                                                                                                                                                                                                           ttCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGatgatg                                                                                                                                                                                <  1:417950/90‑1 (MQ=255)
                                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                   
CCACTCATAGAATGCACGCAGCAGATAGGGACGACGTGGTGTTAGCTGTGACAAATCCATACAGATTAACTCCGGCCCAGACGCATTTCACGTTCTGCTTCAGTTAAAGAAGCAAGGAAAGAGTCACGCTCAAAGACGCGGGTCATATAGCCTTTCAGCTCTTTCGCACCCGGGCCGCTGAACTCGATGCCCAGTTGCGGCAGACGCCACAGCAGCGGAGCAAGATAGCAATCGACCAGGCTGAACTCATCGCTCAGGAAGTACGGCTTCTGACCGAAGACCGGCGCAATCGCCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACG  >  CP009273/3370076‑3370606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑