Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,063,192	C→A	11.7%	intergenic (+49/‑158)	PP_1838 → / → PP_1839	membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,063,192	0	C	A	11.7%	104.2 / 5.5	42	intergenic (+49/‑158)	PP_1838/PP_1839	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (19/18);  new base A (2/3);  total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.04e-01

CAGCCGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGG  >  NC_002947/2063045‑2063340                                                                                                                                                     |                                                                                                                                                     cAGCCGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCa                                                                                                                                                     >  7:248427/1‑149 (MQ=255)   gCCGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCAtt                                                                                                                                                   >  5:290050/1‑149 (MQ=255)      ggAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGca                                                                                                                                                >  2:302606/1‑149 (MQ=255)             gtCAAGAAGCTTGAAGGGTATATCCAGTCCGCGACCAAGAGGCTGCTGGAAAACACCGCCGGGGTGGTTCACGGCACACCGAAGTAAACCGGGGCCGGGTTGCGGCCCATTTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAggg                                                                                                                                           <  1:52164/147‑1 (MQ=255)              tCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAAGGtcc                                                                                                                                        >  4:140408/1‑147 (MQ=255)                aagaagCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCg                                                                                                                                       >  7:152305/1‑148 (MQ=255)                aagaagCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAAGGtcc                                                                                                                                        <  3:140408/147‑3 (MQ=255)                         gAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTtgtg                                                                                                                              <  6:41560/148‑1 (MQ=255)                         gAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGc                                                                                                                             <  1:302606/149‑1 (MQ=255)                            gCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAAGGTCCGAACCCTGTGCaat                                                                                                                          <  8:248427/149‑3 (MQ=255)                                   tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCtgtg                                                                                                                   >  1:80931/1‑149 (MQ=21)                                          cgcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCgg                                                                                                            <  7:111340/149‑1 (MQ=255)                                           gcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCggg                                                                                                           <  8:152305/149‑1 (MQ=255)                                            cgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCTGTGGGAGCGGGc                                                                                                          <  3:142415/149‑1 (MQ=18)                                            cgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTc                                                                                                                                        <  4:154918/119‑1 (MQ=255)                                            cgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTc                                                                                                                                        >  3:154918/1‑119 (MQ=255)                                                   gagCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCTGTGGGAGCGGGCAAGCCcg                                                                                                   <  2:80931/149‑1 (MQ=17)                                                       ctgctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGaa                                                                                               <  1:119621/149‑1 (MQ=255)                                                             gATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTGGGCCCTTGTGCAGGTCCTGTGCGAGCGGGCCAGCCCGGGAATGGGcc                                                                                         >  7:6445/1‑149 (MQ=255)                                                                 acacCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACCGGCATTTCACAGGGTTCGGACCTTGTGGAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCg                                                                                      >  3:79656/1‑148 (MQ=255)                                                                  cacCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTAGCGGGCTTGCCCCCGCCCCCCGGCAATTAACACGGTTGGGACCTTGTGGAGGTTCAGTGGGAGCGGGCAAGCCCGCGCAAGGGGCCCGcc                                                                                    >  4:264903/1‑148 (MQ=255)                                                                   acCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCAt                                                                                                                                                    >  3:162024/1‑84 (MQ=255)                                                                   acCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCAt                                                                                                                                                    <  4:162024/84‑1 (MQ=255)                                                                   acCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCCCAGGGTTCGGACCTTGTGGAGGTCCTGTGCGAGCGGGCAAGCCCGCGGATGGGCCCCGcac                                                                                   >  4:27481/1‑149 (MQ=255)                                                                              ggtgCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCGCCCACAGGCATTTCACACGGTTCCGACCATGTTGAGGGACTGTGCGCGCGGGCAAGCCCCCGAATGGGCCCCGCACAATTTTacccg                                                                        >  4:45485/1‑147 (MQ=37)                                                                                                gTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGc                                                      <  3:45485/149‑1 (MQ=255)                                                                                                   aaCCGGGGCCGCGTTGCGGCCCA‑TTAGCGGGCGTTCCCCCTCCCACAGGCAATGCACAGGGTTACGACCTTGTGCAGGGGCAGTTCGAGGCGGCAAGCCCGCGAAAGGGCCCCGCACAAATTTACCGGAAAGAACATTATACCCGccc                                                    >  4:82370/1‑148 (MQ=255)                                                                                                             gggTTGGGGCCCA‑TTCCGGGGGTTCCCCGCTCCCACCGGAATTGCACAGGGTTCGCCCTTGGTGCTGGGCGGGGGCGCGGGGGAAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGtt                                         <  4:159477/147‑1 (MQ=255)                                                                                                                   cGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCa                                    <  6:290050/148‑1 (MQ=255)                                                                                                                        cA‑TTCGCGGGCTTGCCCGCTCCCCCAGGCATTGCACAGGGTTCGGACCTTGTGGAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATGCCCGCCCCAAGGTCAGTTATTCAGGCATc                              >  7:132423/1‑149 (MQ=255)                                                                                                                             cgcgGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAgg                                               >  5:236599/1‑128 (MQ=255)                                                                                                                             cgcgGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGGCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAgg                                               <  6:236599/128‑1 (MQ=255)                                                                                                                                       cccGCTCCCACAGGCCTTGCACAGGGCTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGtt                <  8:6445/149‑1 (MQ=255)                                                                                                                                        ccGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc               <  3:82370/149‑1 (MQ=255)                                                                                                                                        ccGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc               >  3:112005/1‑149 (MQ=255)                                                                                                                                           cTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCTGTGGGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGtt            >  1:212892/1‑149 (MQ=18)                                                                                                                                             cccACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACaa                                                                                 >  2:266511/1‑78 (MQ=255)                                                                                                                                             cccACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACaa                                                                                 <  1:266511/78‑1 (MQ=255)                                                                                                                                              ccACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc               <  2:295883/143‑1 (MQ=255)                                                                                                                                              ccACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc               >  1:295883/1‑143 (MQ=255)                                                                                                                                                  aGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGTGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAg                                   <  2:100668/119‑1 (MQ=255)                                                                                                                                                  aGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTGCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAg                                   >  1:100668/1‑119 (MQ=255)                                                                                                                                                     cATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAgg  <  4:112005/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CAGCCGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCA‑TTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGG  >  NC_002947/2063045‑2063340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑