Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,857,924	A→C	9.0%	T4T (ACT→ACG)	PP_4272 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,857,924	0	A	C	9.0%	146.1 / 3.2	52	T4T (ACT→ACG)	PP_4272	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (23/24);  new base C (3/2);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCACAGGTCCATCACTACAGTGGCACCAATGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGACAGTTTG  >  NC_002947/4857795‑4858064                                                                                                                                  |                                                                                                                                             ccACAGGTCCATCACTACAGTGGCACCAATGCCAATCCGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAggg                                                                                                                           >  7:211408/1‑149 (MQ=255)         tgaataCTACAGTGGCACCAATGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAAt                                                                                                                   <  8:250917/144‑1 (MQ=255)          cATCACTACAGTGGCACCAATGCCAATCCGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATg                                                                                                                  <  8:211408/149‑1 (MQ=255)             cACTACAGTGGCACCAATGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGa                                                                                                                >  7:178326/1‑148 (MQ=255)              aCTACAGTGGCACCAATGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGAc                                                                                                               <  3:246374/148‑1 (MQ=255)                tACAGTGGCACCAATGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACAtt                                                                                                            >  3:193169/1‑149 (MQ=255)                            aaTGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGcc                                                                                                <  4:193169/149‑1 (MQ=255)                            aaTGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGc                                                                                                 >  3:144576/1‑148 (MQ=255)                                ccAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAAc                                                                                            >  7:58000/1‑149 (MQ=255)                                ccAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTCAACAAGCTATTGAAGGTTGCTGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGTACATTGCCGACGTCGCCAAAc                                                                                            <  1:265705/149‑1 (MQ=255)                                  aaTCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCg                                                                                                                       <  2:50712/120‑1 (MQ=255)                                  aaTCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCg                                                                                                                       >  1:50712/1‑120 (MQ=255)                                   cacgccAAAGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCACTCGAAGGTTGACGAACATTACCATGCCGCGCAGCATAGAAGTTGACGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGCCGTCACCAAACGc                                                                                          >  7:209887/6‑148 (MQ=255)                                                cTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGc                                                                            <  7:148774/149‑1 (MQ=255)                                                   gAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATc                                                                         >  4:132507/1‑149 (MQ=255)                                                    aaaCATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATc                                                                         >  5:300974/1‑148 (MQ=255)                                                            cAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCg                                                                >  5:179963/1‑149 (MQ=255)                                                             aGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGt                                                               <  3:132507/149‑1 (MQ=255)                                                                    gTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTtactac                                                         >  6:21113/1‑148 (MQ=255)                                                                     tCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTTGCGTACCTGCATCGACACTGCGTTAGTACga                                                       <  2:227066/149‑1 (MQ=255)                                                                       aTTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACgag                                                      >  5:13102/1‑148 (MQ=255)                                                                        tttGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACgaga                                                     >  1:314498/1‑148 (MQ=255)                                                                        tttGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGagaa                                                    >  7:260985/1‑149 (MQ=255)                                                                         ttGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACgag                                                      >  8:91773/1‑146 (MQ=255)                                                                             aCAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAg                                               <  8:58000/149‑1 (MQ=255)                                                                                aGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCt                                            >  4:119813/1‑149 (MQ=255)                                                                                   ccTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGc                                         >  8:239711/1‑149 (MQ=255)                                                                                    cTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGc                                         >  6:192458/1‑148 (MQ=255)                                                                                    cTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCt                                        <  5:21113/149‑1 (MQ=255)                                                                                    cTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATACAAGTTCAAGTCAACTTCAAGTCAAGGGCCACAAATGGACATTGCCGCCGGCGCCAAACGCACTGGCGTACCTGCATATAGCCTGAGTTACTACGAGAAGAAAggaatact                                        >  4:238147/1‑143 (MQ=255)                                                                                    cTCGAAGGTTGAATGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAAt                                                                                                                   <  8:234662/74‑1 (MQ=255)                                                                                                 ggTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGcc                           <  2:314498/149‑1 (MQ=255)                                                                                                   tCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCgg                         <  6:210769/149‑1 (MQ=255)                                                                                                   tCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCgg                         >  5:210769/1‑149 (MQ=255)                                                                                                     aTTANCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCgcgc                       >  5:324769/1‑149 (MQ=255)                                                                                                     aTTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCggg                        <  7:239711/148‑1 (MQ=255)                                                                                                     aTTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGgc                       <  8:178326/149‑1 (MQ=255)                                                                                                          cATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCg                                                                <  5:23117/103‑1 (MQ=255)                                                                                                          cATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCg                                                                >  6:23117/1‑103 (MQ=255)                                                                                                          cATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGc                  <  5:192458/149‑1 (MQ=255)                                                                                                               cgcgCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGCGCCCGGCCaagg             <  8:260985/149‑4 (MQ=255)                                                                                                                gcgcAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGt            <  7:91773/149‑1 (MQ=255)                                                                                                                 cgcAGCATAGCAGATGACGTCAACTTCAAGTCAAGGGGCCGAAATGGACTTTGCCGACGTCGCCCACCGAACTGGCGTACCTGCATCTACACTGCGTTACTACGAGAAGAATGGCTTGCGCAAGTCCTTGGCCGCGCCCGGCCaaggac           <  6:308877/149‑6 (MQ=255)                                                                                                                   cagcaTAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGCGCCCGGCCaaggactt         <  6:324769/149‑8 (MQ=255)                                                                                                                       aTAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGACAGt     >  7:181971/1‑149 (MQ=255)                                                                                                                        ttgAAGTTGACTTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGaaa                                                >  4:253277/3‑105 (MQ=255)                                                                                                                        ttgAAGTTGACTTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGGCa       >  6:55569/3‑146 (MQ=255)                                                                                                                        ttgAAGTTGACTTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGACa       <  5:55569/144‑1 (MQ=255)                                                                                                                          gAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGACAGttt   <  4:144576/148‑1 (MQ=255)                                                                                                                          gAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGACAGTTTg  <  6:300974/149‑1 (MQ=255)                                                                                                                              ttGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGc                  >  8:209430/1‑129 (MQ=255)                                                                                                                              ttGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGc                  <  7:209430/129‑1 (MQ=255)                                                                                                                                  |                                                                                                                                             CCACAGGTCCATCACTACAGTGGCACCAATGCCAATCGGCAATGCAGCTAGAAACATCGCAGTAAACGTCATTTGAACAAGCCCTCGAAGGTTGACGGTCATTACCATGCCGCGCAGCATAGAAGTTGAAGTCAACTTCAAGTCAAGGGCCCGAAATGGACATTGCCGACGTCGCCAAACGCACTGGCGTACCTGCATCGACACTGCGTTACTACGAGAAGAAAGGCTTGCTCAAGTCCTTGGCCGGGCGCGGCCAGCGTCGACAGTTTG  >  NC_002947/4857795‑4858064

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: ‑