Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	357,791	C→T	*300* (TAG→TAA)	cynR ←	transcriptional activator of cyn operon, autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,791	0	C	T	96.2%	154.8 / ‑3.7	53	*300* (TAG→TAA)	cynR	transcriptional activator of cyn operon, autorepressor
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (28/23);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 4.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

AGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC  >  NC_000913/357657‑357922                                                                                                                                       |                                                                                                                                    aGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTAcc                                                                                                                                 <  2:158087/139‑1 (MQ=255)     gCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCg                                                                                                                                <  2:1109135/136‑1 (MQ=255)     gCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCg                                                                                                                                >  1:1109135/1‑136 (MQ=255)                              cGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGGCTAATATGCGTAGCGTATCATGTAATTCAGGCCGAAGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAt                                                                                                    <  2:601098/139‑1 (MQ=11)                                gATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCAttt                                                                                                  >  2:1094228/1‑139 (MQ=38)                                 aTGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTa                                                                                                 >  2:431474/1‑139 (MQ=255)                                   gcggcgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATc                                                                                               <  1:431474/139‑1 (MQ=255)                                     ggcgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCa                                                                                             >  2:587620/1‑139 (MQ=255)                                          gAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  1:1094228/139‑1 (MQ=255)                                            aCGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAt                                                                                      <  1:587620/139‑1 (MQ=255)                                                         ccTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGcc                                                                         >  1:904262/1‑139 (MQ=255)                                                         ccTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         <  2:960389/107‑1 (MQ=255)                                                         ccTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         >  1:960389/1‑107 (MQ=255)                                                          cTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCt                                                                        >  1:410643/1‑139 (MQ=255)                                                              gTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTcgc                                                                    >  2:642723/1‑139 (MQ=255)                                                                  agCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCgcggc                                                                 >  1:932938/1‑138 (MQ=255)                                                                  agCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCgcggc                                                                 <  2:932938/138‑1 (MQ=255)                                                                       tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGt                                                           >  1:494659/1‑139 (MQ=255)                                                                             cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCa                                                     >  1:1085938/1‑139 (MQ=255)                                                                                     tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGcggcgg                                                               >  1:574195/1‑121 (MQ=255)                                                                                     tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGAAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGcggcgg                                                               <  2:574195/121‑1 (MQ=255)                                                                                        tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         <  1:87101/76‑1 (MQ=255)                                                                                        tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         >  2:87101/1‑76 (MQ=255)                                                                                          aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                        <  2:410643/139‑1 (MQ=255)                                                                                            cGTAGCGCATCGGGCAATCCCAGCCGCAGAACTCGGTCAGCTGCTACCGGGCTTCTTTTCCGCCAACAACCTCGCATTTATCCAACGCCTTGTGCAAAAAAGCCTTCGCGGCGGCTGTCAGCAAGATATTTTTgcgcca                                      >  2:1095855/1‑138 (MQ=255)                                                                                            cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         >  2:24472/1‑72 (MQ=255)                                                                                            cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         <  1:24472/72‑1 (MQ=255)                                                                                            cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                      >  2:1036033/1‑139 (MQ=255)                                                                                                 cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCa                                                                                       <  1:494530/85‑1 (MQ=255)                                                                                                 cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCa                                                                                       >  2:494530/1‑85 (MQ=255)                                                                                                     tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                             >  2:532664/1‑139 (MQ=255)                                                                                                      cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaac                                                                                                              <  1:91901/57‑1 (MQ=255)                                                                                                      cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCcaac                                                                                                              >  2:91901/1‑57 (MQ=255)                                                                                                      cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                            >  2:45511/1‑139 (MQ=255)                                                                                                       aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                           <  1:919118/139‑1 (MQ=255)                                                                                                            aTTCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt                      <  1:1036033/139‑1 (MQ=255)                                                                                                             ttCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCa                                                     <  1:1063559/107‑1 (MQ=255)                                                                                                             ttCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCa                                                     >  2:1063559/1‑107 (MQ=255)                                                                                                              tCCAGCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                    >  2:167861/1‑139 (MQ=255)                                                                                                                  gCCGCAGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                >  1:681078/1‑139 (MQ=255)                                                                                                                       aGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAtgt                                                                                    <  1:900307/66‑1 (MQ=255)                                                                                                                       aGACCTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAtgt                                                                                    >  2:900307/1‑66 (MQ=255)                                                                                                                        gatcTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         <  1:898503/41‑1 (MQ=255)                                                                                                                        gatcTGTGTCAGCGGTTACCGTGATTCATTTCCGCCAACAACcg                                                                                                         >  2:898503/4‑44 (MQ=11)                                                                                                                               gtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTcgcag                                                                  <  1:632673/76‑3 (MQ=255)                                                                                                                               gtCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTcgcag                                                                  >  2:632673/1‑74 (MQ=255)                                                                                                                                tCAGCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc  >  1:335001/1‑139 (MQ=255)                                                                                                                                   gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        <  1:118411/50‑1 (MQ=255)                                                                                                                                   gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGcc                                                                                        >  2:118411/1‑50 (MQ=255)                                                                                                                                   gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGc                                                       <  1:755316/83‑1 (MQ=255)                                                                                                                                   gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGc                                                       >  2:755316/1‑83 (MQ=255)                                                                                                                                   gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCt                                                  <  2:577042/88‑1 (MQ=255)                                                                                                                                   gCGGTTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCt                                                  >  1:577042/1‑88 (MQ=255)                                                                                                                                       |                                                                                                                                    AGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC  >  NC_000913/357657‑357922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑