Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	6,089,343	0	A	C	33.3%	68.9 / 11.3	55	S192R (AGC→CGC)	paiB	Protease synthase and sporulation protein PAI 2
Reads supporting (aligned to +/- strand):  ref base A (25/11);  new base C (1/17);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 6.81e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CCCCTGCCGACTACATCGAGGGCATGCTCCGCGCCATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTGGCACGCCCT  >  ACB143/6089209‑6089469                                                                                                                                       |                                                                                                                               ccccTGCCGACTACATCGAGGGCATGCTCCGCGCCATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGa                                                                                                                                >  2:117839/1‑135 (MQ=255)                   aGGGCATGCTCCGCGCCATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAAc                                                                                                              >  7:12834/1‑135 (MQ=255)                           cTCCGCGCCATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACaa                                                                                                       >  8:126718/1‑134 (MQ=255)                            tCCGCGCCATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGCCATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAAt                                                                                                      >  7:282640/1‑134 (MQ=255)                                   cATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTcgc                                                                                              >  4:121725/1‑135 (MQ=255)                                   cATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTcgc                                                                                              >  1:84977/1‑135 (MQ=255)                                               ccGGCTGCCCCCCCCGCGCCTGCACGGGGCGCGCAAGCTCCCCCCGACCCGCTCCGGGCACGCCCGCGCGGGGGCGCCCCCCCCCCCCCCCCCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATgc                                                                                   <  4:147215/134‑1 (MQ=255)                                                     gccccgcgcgcgCCGGCCCGGGGCGCGCCAGCCCAGCCCGACCCGCTCCGGGCACGACAGCGCGGGGGGGCGCGCCGGCCCCCCCCCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAAct                                                                            <  8:207705/129‑1 (MQ=255)                                                      ccccccgcgcgCCTGCACGGGGCGCGCAAGCCCAGCCCGACCCGCTCCGGGCAAGCCACCGCGGGCGGGCGCGCCCCCCGCCCCCCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAActc                                                                           <  8:29006/130‑1 (MQ=255)                                                      cccAGCGCGCGCCTGCTCGGGGCGCGCAAGCGCCGCCAGCCCCGCTCCGGGCAAGACATCGCTGGGGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAAct                                                                            <  6:88124/134‑1 (MQ=255)                                                         aTCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAActct                                                                          >  3:339071/1‑133 (MQ=255)                                                         aTCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAActct                                                                          >  1:353882/1‑133 (MQ=255)                                                         aTCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTg                                                                         >  5:228768/1‑134 (MQ=255)                                                         aTCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGAGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAActct                                                                          >  1:92235/1‑133 (MQ=255)                                                            gcgcgcCTGCATGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACAGCGCTGGTGGGCGCGAAGGCCGGCGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAgg                                                                     <  2:112435/135‑1 (MQ=255)                                                              ccgggtGCACGGGGCGCGCCAGCTCAGCCCCCCCCGCGCCGGGCACGACAGCGCGGGTGGCCCCGACGCCCCCCCCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAAt                                                                  <  6:228768/131‑1 (MQ=255)                                                                gcggccAAGGTGCGGGTATGCTCAGCAATAAGCGGTCCGGTCAAGATCTCTCTGGTGTGCGCCAAGGCCTGCCCCCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATa                                                                 <  2:178332/130‑1 (MQ=255)                                                                   tGCACGGTGCGCGCAAGCGCCGCCAGCACGGCTCCGGGCAACCCATCGGTGGGGTGCGCGACGGCCTGCGCCCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGccc                                                             <  6:952/136‑1 (MQ=255)                                                                   tGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGc                                                               >  2:18385/1‑134 (MQ=255)                                                                     gccggTCCGCGCAAGCCCACCCAGCCCCGCTCCGGTCACGACTGCGCGGGGGCGCGCCCACGCCCCCCCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  5:201396/133‑1 (MQ=255)                                                                     cAAGGTGCTCTCAAGCTCAGCCAGAACCGCTCCGGTCAAGACTTCGCTGGTGGGCGCGATGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  6:324077/136‑1 (MQ=255)                                                                      tcggTGCGCGCAAGCTCAGCCAGAACCGCTCGGGGCAAGACATCGCGGGTGGGCGCCAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  7:184950/133‑1 (MQ=255)                                                                      ctggggcgcgcACGCACCGCCCCACCCGCGCCGGGCACGCCATCGCGGGCGGGCGCTACGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  2:305562/130‑1 (MQ=255)                                                                      caGGTGCGCGCAAGCTCAGCCACACCCGCTCCGGGCAAGACAGCGCTGGGGCGCCCGCACCCCCCCCCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  7:63600/134‑1 (MQ=255)                                                                      atggTGCGCGCAAGCTCAGCCAGACCCGCTCCGGCCACGACATCGCTGGGGTGCGCTAAGGCCTGCCCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  4:40192/133‑1 (MQ=255)                                                                      agggTGCGCGCATCCGCCGCCCCAACCGCTCCGGGCAAGACATCGCGGGTGCGCGCGAAGGCCGGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  3:3348/133‑1 (MQ=255)                                                                      aaGGTGCGCGCCAGCGCAGCCAGAACCGCTCGGTGCATGCAATCGCGGGGCGGCGCGACGGCCCGCCCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  7:127934/135‑1 (MQ=255)                                                                      aaGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGTGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           <  4:120342/135‑1 (MQ=255)                                                                      aaGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGAGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCAt                                                           >  1:346074/1‑135 (MQ=255)                                                                          tGCGCGAAAGATCAGCCAGAACCGCTCCGGGCAAGCCATCGCTGGTGTGCGCGAAGGCCTGCGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCa                                                      <  6:106581/136‑1 (MQ=255)                                                                             gcgcAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGcccca                                                     >  1:215675/1‑132 (MQ=255)                                                                             gcgcAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAAc                                                    >  2:351717/1‑135 (MQ=255)                                                                               gcAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGACGGCCTGAGCGCCAGCCCCGATCACCTGGACAATCAACTCGCGGCGCACCTGCGCCAACTCTGAAGGAATAGCCCCTGCCCAACCt                                                  >  7:234593/1‑135 (MQ=255)                                                                               gcAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAAcc                                                   >  4:371476/1‑134 (MQ=255)                                                                               gcAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAAcc                                                   >  7:239687/1‑134 (MQ=255)                                                                                     tCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTg                                           >  5:2844/1‑136 (MQ=255)                                                                                       aGCCCGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGCCCTGACCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTgc                                          <  7:160513/135‑1 (MQ=255)                                                                                             aagcGCTGCGGGCAAGTCATCGGCGGGGCGCCCCAAGGCCGCCGCGCAAGCCCGGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTg                                    <  5:257006/132‑1 (MQ=255)                                                                                             aaCCGCGCCGGGCAAGTATGTGGTGGGGTGCGCTATGGCCTGTGCCCAAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTg                                    <  2:396650/135‑1 (MQ=255)                                                                                             aaCCGCGCCGGGCAACACAGCGGGGGGGTGCGCTAAGGCCTCAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTg                                    <  2:104131/135‑1 (MQ=255)                                                                                             aaCCGCCCCGGGCAATACATCGGTGGTGGGCGCGAAGGCCTCAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTg                                    <  4:269800/135‑1 (MQ=255)                                                                                                cGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCa                                 >  7:258012/1‑135 (MQ=255)                                                                                                    ccGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCCACTCTGAATGAATAGCCCATGCCCAACAGTACCCTGCGCCCTGTCACGGc                             >  3:154457/1‑135 (MQ=255)                                                                                                    ccGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGc                             >  1:300152/1‑135 (MQ=255)                                                                                                      gggCAAGCCATCGCTGGTGTGCGCGAAGGCCTGCGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCACCTCAGAAGGAATAGCCCATGCCCCACCTTACCCTGCGCCCTGTCACGGccc                           >  1:408050/1‑135 (MQ=255)                                                                                                            gACATGGCTGGGGGGCGCGCAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATc                     <  7:385948/135‑1 (MQ=255)                                                                                                               aTCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCACCTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGCTCCCGc                 >  5:124351/1‑136 (MQ=255)                                                                                                                tggCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGTAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGc                 <  7:184916/133‑1 (MQ=255)                                                                                                                     ggTGTGCGCGACCGCCTGCGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTg           <  5:118784/136‑1 (MQ=255)                                                                                                                      gtgtGCGCGTAGCCCTCCCCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTg           <  8:112404/135‑1 (MQ=255)                                                                                                                      gggcgcgcgcCGGCCCGCGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTg           <  3:108893/131‑1 (MQ=255)                                                                                                                       tgggcgcGAAGGCCCGCGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTg           <  4:105360/131‑1 (MQ=255)                                                                                                                          gcgcGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTGGCAc       >  4:387052/1‑135 (MQ=255)                                                                                                                            gcgAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTGGCACGc     >  1:26373/1‑135 (MQ=255)                                                                                                                              gAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCCCGCAGCCTGGCACGCCCt  >  5:177154/1‑136 (MQ=255)                                                                                                                              gAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTGGCACGCCCt  >  6:348386/1‑136 (MQ=255)                                                                                                                                       |                                                                                                                               CCCCTGCCGACTACATCGAGGGCATGCTCCGCGCCATCGTCGGTATCCGTCTGCCCATCGCGCGCCTGCAAGGTGCGCGCAAGCTCAGCCAGAACCGCTCCGGGCAAGACATCGCTGGTGTGCGCGAAGGCCTGAGCGCCAGCCCCGATCAACTGGACAATCAACTCGCGGCGCACATGCGCCAACTCTGAAGGAATAGCCCATGCCCAACCTTACCCTGCGCCCTGTCACGGCCCAAGATCACGCAGCCTGGCACGCCCT  >  ACB143/6089209‑6089469

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑