Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,068,298	0	A	C	71.4%	101.3 / 56.7	63	A13A (GCA→GCC)	BW25113_RS10450	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (10/8);  new base C (25/20);  total (35/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.05e-02
Rejected as consensus: Frequency below/above cutoff threshold.

TCCCGGTCATCATGACCGGGACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGAACGCATAACCCGG  >  NZ_CP009273/2068162‑2068427                                                                                                                                         |                                                                                                                                  tCCCGGTCATCATGACCGGGACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAg                                                                                                                                  >  2:525915/1‑138 (MQ=255)      gTCATCATGACCGGGACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTg                                                                                                                            >  1:115429/1‑139 (MQ=255)      gTCATCATGACCGGGACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTg                                                                                                                            >  1:678921/1‑139 (MQ=255)               aCCGGGACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCAttcttc                                                                                                                   <  2:30675/139‑1 (MQ=255)                 cGGGGCCCGGACAGGCGCAACGGATCTTCAACGCCACATTCGATGGCATTAACAATAACCTGATATTCATCACGGAGTGACAATGGTACAGATAGTCGGCGCGCTGATCATGCTGATCGCCGGATTTGCCATTCTTCGc                                                                                                                 >  2:617401/1‑139 (MQ=255)                   ggACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCt                                                                                                               >  2:8511/1‑139 (MQ=255)                    gACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCtt                                                                                                              >  1:95661/1‑139 (MQ=255)                     aCCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCttt                                                                                                             >  1:269049/1‑139 (MQ=255)                         ggACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGtt                                                                                                         <  1:525915/139‑1 (MQ=255)                          gACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTc                                                                                                        <  1:217740/139‑1 (MQ=255)                           aCCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCa                                                                                                       <  2:841250/139‑1 (MQ=255)                              ggCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCagag                                                                                                    >  1:774279/1‑139 (MQ=255)                                cgcAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCa                                                                                                  <  1:227532/139‑1 (MQ=255)                                      ggATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATc                                                                                            <  2:115429/139‑1 (MQ=255)                                             cAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCa                                                                                        <  2:774279/136‑1 (MQ=255)                                                   cacaTTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTg                                                                               >  2:169587/1‑139 (MQ=255)                                                          gCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGc                                                                        <  1:8511/139‑1 (MQ=255)                                                           cTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTgg                                                                         >  2:440994/1‑137 (MQ=255)                                                           cTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTgg                                                                         >  2:163390/1‑137 (MQ=255)                                                               cATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGc                                                                   <  1:212653/139‑1 (MQ=255)                                                                               atatTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCt                                                   >  1:150303/1‑139 (MQ=255)                                                                                tatTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTg                                                  >  2:610233/1‑139 (MQ=255)                                                                                tatTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGc                                                          <  2:230814/131‑1 (MQ=255)                                                                                tatTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGc                                                          >  1:230814/1‑131 (MQ=255)                                                                                  ttCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAgg                                                                     <  1:431010/118‑1 (MQ=255)                                                                                  ttCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAgg                                                                     >  2:431010/1‑118 (MQ=255)                                                                                     atcaCGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTcgg                                             >  1:663324/1‑139 (MQ=255)                                                                                      tcaCGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTcggc                                            >  1:793896/1‑139 (MQ=255)                                                                                       caCGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTcggcc                                           >  2:363492/1‑139 (MQ=255)                                                                                        aCGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTcggcc                                           <  1:440994/138‑1 (MQ=255)                                                                                            aGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTcggcccggcc                                      >  1:657473/1‑139 (MQ=255)                                                                                                aCTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCa                                                                                        <  1:28267/85‑1 (MQ=255)                                                                                                aCTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCa                                                                                        >  2:28267/1‑85 (MQ=255)                                                                                                    tGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActgg                               <  1:675061/138‑1 (MQ=255)                                                                                                      ttACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCtgtg                                                      <  2:467296/113‑1 (MQ=255)                                                                                                      ttACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCtgtg                                                      >  1:467296/1‑113 (MQ=255)                                                                                                      ttACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActggctg                            >  1:814018/1‑139 (MQ=255)                                                                                                      ttACAGATAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActggct                             <  1:810822/138‑1 (MQ=255)                                                                                                        aCAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACtggctggc                          >  2:776780/1‑139 (MQ=255)                                                                                                            aTAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCa                                                                                                  >  2:121192/1‑63 (MQ=255)                                                                                                            aTAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCa                                                                                                  <  1:121192/63‑1 (MQ=255)                                                                                                            aTAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCtata                      >  1:670027/1‑139 (MQ=255)                                                                                                            aTAGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCtata                      >  1:342978/1‑139 (MQ=255)                                                                                                              aGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCAttcttc                                                                                                                   >  2:102811/1‑44 (MQ=255)                                                                                                              aGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCAttcttc                                                                                                                   <  1:102811/44‑1 (MQ=255)                                                                                                              aGTCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTatat                     >  1:697419/1‑138 (MQ=255)                                                                                                                tCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGt                                                 <  2:843764/108‑1 (MQ=255)                                                                                                                tCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGt                                                 >  1:843764/1‑108 (MQ=255)                                                                                                                tCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActggct                             <  2:347477/128‑1 (MQ=255)                                                                                                                tCGGCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActggct                             >  1:347477/1‑128 (MQ=255)                                                                                                                tCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActggctgg                           >  2:29986/1‑130 (MQ=255)                                                                                                                tCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTActggctgg                           <  1:29986/130‑1 (MQ=255)                                                                                                                  ggCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCg                <  2:342978/139‑1 (MQ=255)                                                                                                                  ggCGCGCTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCg                <  1:163390/139‑1 (MQ=255)                                                                                                                  ggCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCg                <  2:95661/139‑1 (MQ=255)                                                                                                                    cgcgcTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGaa              >  2:396471/1‑139 (MQ=255)                                                                                                                      cgcTGATCCTGCTGATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGAACg            >  2:836105/1‑139 (MQ=255)                                                                                                                                 ctgATCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGAACGCATAACCCgg  <  1:396471/138‑1 (MQ=255)                                                                                                                                 ctaaTCGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGAACGCATACCCCgg  <  2:271828/135‑1 (MQ=255)                                                                                                                                      cGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGa               <  2:371314/120‑1 (MQ=255)                                                                                                                                      cGCCGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGa               >  1:371314/1‑120 (MQ=255)                                                                                                                                       gCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCAc                                                                                       >  2:264756/1‑47 (MQ=255)                                                                                                                                       gCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCAc                                                                                       <  1:264756/47‑1 (MQ=255)                                                                                                                                         |                                                                                                                                  TCCCGGTCATCATGACCGGGACCCGGACCGGCGCAACGGATCTTCAACGCCACATTCGCTGGCATTAACAATAACATGATATTCATCACGGAGTGACTATGTTACAGATAGTCGGCGCGCTGATCCTGCTGATCGCAGGATTTGCCATTCTTCGCCTTTTGTTCAGAGCATTAATCAGCACGGCTTCTGCGCTGGCAGGGCTCATATTGCTGTGTCTGTTCGGCCCGGCCTTACTGGCTGGCTATATCACCGAACGCATAACCCGG  >  NZ_CP009273/2068162‑2068427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑