Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,845,783	T→C	14.6%	L25P (CTC→CCC)	pfeS‑II →	histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,845,783	0	T	C	14.6%	109.0 / 11.0	48	L25P (CTC→CCC)	pfeS‑II	histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (19/22);  new base C (3/4);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

GTTATCACGAACGGCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCAT  >  NC_002947/1845636‑1845930                                                                                                                                                    |                                                                                                                                                    gTTATCACGAACGGCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCt                                                                                                                                                     >  3:191367/1‑148 (MQ=255)              gCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTggg                                                                                                                                       <  4:127956/149‑1 (MQ=255)                aGATTCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGc                                                                                                                                     <  2:128246/149‑1 (MQ=255)                aGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGc                                                                                                                                     <  7:31660/149‑1 (MQ=255)                     cGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGc                                                                                                                                 >  6:70678/1‑148 (MQ=255)                     cGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGc                                                                                                                                 <  5:70678/148‑1 (MQ=255)                      gCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGca                                                                                                                                >  8:331058/1‑148 (MQ=255)                          cGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTTAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATgg                                                                                                                           <  6:144103/149‑1 (MQ=255)                                gggCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAAccc                                                                                                                     <  5:27712/149‑1 (MQ=255)                                  gCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAAcc                                                                                                                      >  4:233307/1‑146 (MQ=255)                                           aCGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCtt                                                                                                           <  2:257681/148‑1 (MQ=255)                                            cGTGCTCAGTGCCAGCGAGGCTGAGTGTACCATTCTCGACGGCCTTTCGCTGTTCTTGAAGCTGGCCATCTTTCTGGTGGGATTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGTAACCCAGAATGCCTTc                                                                                                          <  7:321411/148‑1 (MQ=255)                                            cGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTc                                                                                                          <  4:191367/148‑1 (MQ=255)                                             gTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCct                                                                                                        >  5:338536/1‑149 (MQ=255)                                                   aGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCg                                                                                                    >  7:176347/1‑147 (MQ=255)                                                   aGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGa                                                                                                  <  7:205478/149‑1 (MQ=255)                                                     tGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGc                                                                                                <  6:253921/149‑1 (MQ=255)                                                      gCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGtt                                                                                                                                                <  2:45142/100‑1 (MQ=255)                                                      gCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGtt                                                                                                                                                >  1:45142/1‑100 (MQ=255)                                                               gCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGGGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCa                                                                                      <  6:287758/149‑1 (MQ=255)                                                                  gAGTGATCGATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCTTCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCGTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCGGGCACGCCAGAc                                                                                   <  1:62422/149‑1 (MQ=255)                                                                  gAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGc                                                                                                                                     >  4:318819/1‑99 (MQ=255)                                                                  gAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCCCAGGTATAACTGAGGc                                                                                                                                     <  3:318819/99‑1 (MQ=255)                                                                         ccATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCgg                                                                            >  5:172732/1‑149 (MQ=255)                                                                              cTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGtt                                                                        <  8:176347/148‑1 (MQ=255)                                                                               tCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTAt                                                                      >  4:36061/1‑149 (MQ=255)                                                                                 gACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATgc                                                                    >  5:220695/1‑149 (MQ=255)                                                                                    cGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGt                                                                         <  5:239221/141‑1 (MQ=255)                                                                                    cGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGt                                                                         >  6:239221/1‑141 (MQ=255)                                                                                    cGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATgccgc                                                                 <  7:331058/149‑1 (MQ=255)                                                                                    cGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATgccgc                                                                 >  6:126016/1‑149 (MQ=255)                                                                                             cTGTTCTGGAAGCAGGCCATCTTGCTGGTGGGCTTCAGCCTCCTGATGATCCGCCTCAGAAATAAATGGGGCCGCCACATGGAAACCCAGAAAGACTTCCACTCGGAGCCGGCACGCCAGACCAAGCGGGGTGATGCCGCCGAAGCTg                                                         >  8:322949/1‑148 (MQ=255)                                                                                              tGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGaa                                                       >  5:247002/1‑149 (MQ=255)                                                                                                          tGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGgcg                                            <  3:233307/148‑1 (MQ=255)                                                                                                             ccATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATg                                                                                                                            >  2:201098/1‑65 (MQ=255)                                                                                                             ccATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGCCCTCAGTTATACCTGGGGCCGGCACATg                                                                                                                            <  1:201098/65‑1 (MQ=255)                                                                                                                       ggtggGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATgccgc                                                                 <  5:31003/114‑1 (MQ=255)                                                                                                                       ggtggGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATgccgc                                                                 >  6:31003/1‑114 (MQ=255)                                                                                                                        gtggGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGgcgggcgg                               <  6:220695/147‑1 (MQ=255)                                                                                                                        gtggGCATCTGCCTGCTGCTGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTCCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGcgggcggg                              >  6:113824/1‑148 (MQ=255)                                                                                                                         tggGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCa                            <  3:36061/149‑1 (MQ=255)                                                                                                                          gggCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGc                                                  >  4:49467/1‑126 (MQ=255)                                                                                                                          gggCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGc                                                  <  3:49467/126‑1 (MQ=255)                                                                                                                              ttCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGAGGGGTAATGCCGACGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCt                       >  5:149722/1‑149 (MQ=255)                                                                                                                                      gctgATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAgt               >  8:333714/1‑149 (MQ=255)                                                                                                                                          tgtgccGGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAgtgggt           >  6:20136/6‑149 (MQ=255)                                                                                                                                               cGGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAgtgg             <  4:353532/142‑1 (MQ=255)                                                                                                                                               cGGCCCCAGGTATAACTGAGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAgtgg             >  3:353532/1‑142 (MQ=255)                                                                                                                                                   cTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCAt  <  6:172732/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GTTATCACGAACGGCAGATCCGCACCGTGTGGGGCAAGGGTTACGTGCTCAGTGCCAGCGAGGCGGAGTGAACCATGCTCGACCGCCATTCGCTGTTCTGGAAGCTGGCCATCTTGCTGGTGGGCTTCTGCCTGCTGATGATCGGCCTCAGTTATACCTGGGGCCGGCACATGGAAACCCAGAATGCCTTCCTCTCGGAGCCGGCACGCCAGACCTTGCGGGGTTATGCCGCCGAAGCTGAACAGGCCTGGCGCAGTGGCGGGCGGGCAGGGCTGGACCAGTGGGTGGCGGCCAT  >  NC_002947/1845636‑1845930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑