Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,845,787	T→G	12.7%	S26R (AGT→AGG)	pfeS‑II →	histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,845,787	0	T	G	12.7%	147.3 / 12.8	55	S26R (AGT→AGG)	pfeS‑II	histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (27/21);  new base G (3/4);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

ACGAACGGCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCATGCATC  >  NC_002947/1845642‑1845935                                                                                                                                                  |                                                                                                                                                      aCGAACGGCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTta                                                                                                                                                     <  8:295881/148‑1 (MQ=255)          aGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGACGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGc                                                                                                                                           <  1:109393/149‑1 (MQ=255)            aTCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGcc                                                                                                                                          >  2:380931/1‑148 (MQ=255)              ccGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGCCga                                                                                                                                        <  1:380931/148‑2 (MQ=255)                 cACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGcaca                                                                                                                                    >  2:79300/1‑149 (MQ=255)                          gggCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGCCCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGAGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAAcc                                                                                                                            >  6:230809/1‑148 (MQ=255)                          gggCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAAcc                                                                                                                            <  6:307515/148‑1 (MQ=255)                          gggCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAAcc                                                                                                                            >  2:32914/1‑148 (MQ=255)                                   ttACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCt                                                                                                                  <  5:19967/149‑1 (MQ=255)                                         gCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCctct                                                                                                            >  6:107547/1‑149 (MQ=255)                                               taccAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑c                                                                                                     <  5:334200/147‑1 (MQ=255)                                                    gCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCa                                                                                                >  7:171475/1‑149 (MQ=255)                                                         gCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGc                                                                                             >  8:191874/1‑147 (MQ=255)                                                           ggAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGGTGGTGCGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGTGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGa                                                                                         <  5:227042/149‑1 (MQ=255)                                                            gAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGAc                                                                                        >  1:137738/1‑149 (MQ=255)                                                              gTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCgg                                                                                                  <  6:156187/137‑1 (MQ=255)                                                              gTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCgg                                                                                                  >  5:156187/1‑137 (MQ=255)                                                                 aaCCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCGTTCCTCTCGGAG‑CCGGCACGCCAGACCTTg                                                                                    <  1:32914/148‑1 (MQ=255)                                                                   ccATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCAc                                                                                               <  7:336999/135‑1 (MQ=255)                                                                   ccATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCAc                                                                                               >  8:336999/1‑135 (MQ=255)                                                                    cATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCggg                                                                                <  4:265973/149‑1 (MQ=255)                                                                    cATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCggg                                                                                >  2:26117/1‑149 (MQ=255)                                                                    cATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCggg                                                                                >  7:76325/1‑149 (MQ=255)                                                                      tGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGt                                                                              >  3:172654/1‑149 (MQ=255)                                                                         tCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTAt                                                                           >  1:59648/1‑149 (MQ=255)                                                                           gACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTAt                                                                           <  8:171475/147‑1 (MQ=255)                                                                                  aTTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGccgccg                                                                    >  5:169081/1‑147 (MQ=255)                                                                                   ttCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAg                                                                 >  8:202121/1‑149 (MQ=255)                                                                                    tCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGc                                                                >  5:154161/1‑149 (MQ=255)                                                                                            cTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAg                                                         <  7:191874/148‑1 (MQ=255)                                                                                                aaGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACGTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTg                                                    <  7:202121/149‑1 (MQ=255)                                                                                                            ttGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTggcgg                                        >  5:115885/1‑149 (MQ=255)                                                                                                             tGCTGGTGGGCTTCTGCCTGCTGATGGTCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGc                                                                                                                    >  1:203388/1‑73 (MQ=255)                                                                                                             tGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGc                                                                                                                    <  2:203388/73‑1 (MQ=255)                                                                                                               cTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTggcgggcg                                     >  3:194824/1‑149 (MQ=255)                                                                                                                tggtggGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGgcgggcgg                                    <  4:172654/149‑1 (MQ=255)                                                                                                                  gtggGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGcgggcggg                                   >  8:47501/1‑148 (MQ=255)                                                                                                                    ggccTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAg                                <  3:71569/146‑1 (MQ=255)                                                                                                                        ctCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTggcgg                                        <  6:281214/136‑1 (MQ=255)                                                                                                                        ctCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTggcgg                                        >  5:281214/2‑137 (MQ=255)                                                                                                                             cctgcTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTgg                          <  5:230809/146‑1 (MQ=255)                                                                                                                             cctgcTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGAc                        <  6:115885/148‑1 (MQ=255)                                                                                                                               tgctgATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAg                     >  2:238707/1‑149 (MQ=255)                                                                                                                                 ctgATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAgt                    <  6:154161/148‑1 (MQ=255)                                                                                                                                    tgtgccGGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAgtgggt                >  7:8824/6‑149 (MQ=255)                                                                                                                                     tGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTg               >  6:122488‑M2/1‑148 (MQ=255)                                                                                                                                       aTCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTggc             >  1:26117‑M2/1‑146 (MQ=255)                                                                                                                                        ccgGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAAAGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTggcg            <  1:78219‑M2/148‑5 (MQ=255)                                                                                                                                        ccGGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGaa                                                                  <  1:248584/95‑1 (MQ=38)                                                                                                                                        ccGGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGaa                                                                  >  2:248584/2‑95 (MQ=39)                                                                                                                                            ccTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCacccactggtccagccctgcccgcccgccactgcgccaggcctgttcagcttcggcggcat        <  5:107547‑M1/149‑62 (MQ=255)                                                                                                                                            ccTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCacccactggtccagccctgcccgcccgccactgcgccaggcctgttcagcttcggcggca         >  8:289359‑M1/1‑88 (MQ=255)                                                                                                                                             cTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCAt       >  7:30371/1‑149 (MQ=255)                                                                                                                                              tCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCATg      >  3:144115/1‑149 (MQ=255)                                                                                                                                                aGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCacccactggtccagccctgcccgcccgccactgcgccaggcctgttcagcttcggcggcataa      <  7:289359‑M1/147‑64 (MQ=255)                                                                                                                                                  ttATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCATGCATc  >  7:288746/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                      ACGAACGGCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAG‑CCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCATGCATC  >  NC_002947/1845642‑1845935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑