Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,608,294	T→A	12.7%	intergenic (‑156/+32)	cyaB ← / ← waaA	cyclolysin secretion/processing ATP‑binding protein CyaB/3‑deoxy‑D‑manno‑octulosonic acid transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,608,294	0	T	A	12.7%	122.5 / 7.8	47	intergenic (‑156/+32)	cyaB/waaA	cyclolysin secretion/processing ATP‑binding protein CyaB/3‑deoxy‑D‑manno‑octulosonic acid transferase
Reads supporting (aligned to +/- strand):  ref base T (19/22);  new base A (3/3);  total (22/25)
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

TCCCACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCACC  >  NC_002947/5608150‑5608440                                                                                                                                                  |                                                                                                                                                   tCCCACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGAc                                                                                                                                                >  6:138335/1‑149 (MQ=255)    cacaAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCgg                                                                                                                                             <  7:237501/149‑1 (MQ=255)    cacaAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCgg                                                                                                                                             <  5:132718/149‑1 (MQ=255)     acaAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACTACTTAGGCCGTAGGAATAAATATCCAGAATCAGACATATCCACTC‑TAGACCggg                                                                                                                                            >  6:236979/1‑149 (MQ=255)      caAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCggg                                                                                                                                            >  8:245674/1‑148 (MQ=255)              cGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTCtagag                                                                                                                                     <  7:170116/148‑5 (MQ=255)                 cGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTT‑CAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGat                                                                                                                               <  5:30569/149‑1 (MQ=255)                           tgACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGt                                                                                                                       >  8:19712/1‑148 (MQ=255)                               acTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTAt                                                                                                                    >  3:147174/1‑147 (MQ=255)                                      aCTTTTAAAGTCTTTTAGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATGAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATc                                                                                                           <  6:79240/149‑1 (MQ=255)                                        ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTC‑TAGAGTGGata                                                                                                                              <  6:1246/128‑1 (MQ=38)                                        ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTC‑TAGAGTGGata                                                                                                                              >  5:1246/1‑128 (MQ=38)                                        ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGa                                                                                                                                     >  1:160242/1‑121 (MQ=255)                                        ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGa                                                                                                                                     <  2:160242/121‑1 (MQ=255)                                        ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATc                                                                                                           >  8:37576/1‑147 (MQ=255)                                        ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCaa                                                                                                         >  8:67119/1‑149 (MQ=255)                                                    ttCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGAc                                                                                              <  7:245674/148‑1 (MQ=255)                                                       gTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGt                                                                                                                       <  8:145694/120‑1 (MQ=255)                                                       gTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGt                                                                                                                       >  7:145694/1‑120 (MQ=255)                                                        tAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTC‑TAGAGTGGATATGTc                                                                                                                          >  6:146872/1‑116 (MQ=37)                                                        tAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTC‑TAGAGTGGATATGTc                                                                                                                          <  5:146872/116‑1 (MQ=37)                                                          ggAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAg                                                                                       <  4:106625/149‑1 (MQ=255)                                                                   cTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCttt                                                                                                                                       >  4:218772/1‑92 (MQ=255)                                                                   cTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCttt                                                                                                                                       <  3:218772/92‑1 (MQ=255)                                                                   cTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCt                                                                               <  7:67119/148‑1 (MQ=255)                                                                   cTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTg                                                                              <  5:138335/149‑1 (MQ=255)                                                                       cGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCaaa                                                                          <  4:183969/149‑1 (MQ=255)                                                                         gCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGc                                                                        >  1:22365/1‑149 (MQ=255)                                                                         gCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGc                                                                        >  7:41438/1‑149 (MQ=255)                                                                                aTCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGa                                                                 <  4:147174/149‑1 (MQ=255)                                                                                aTCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGa                                                                 <  3:108141/149‑1 (MQ=255)                                                                                   taGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCa                                                                                                                  <  4:187632/96‑1 (MQ=255)                                                                                   aaGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCa                                                                                                                  >  3:187632/2‑97 (MQ=255)                                                                                    aGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTgg                                                             >  2:275470/1‑149 (MQ=255)                                                                                           gAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGCCCCTCGAGCAATCGCTGCATCGCCCCCTGATTGGCCCGCAt                                                      >  8:114777/1‑149 (MQ=255)                                                                                                                ggAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCAc                                  <  7:37576/148‑1 (MQ=255)                                                                                                                  aataaataACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCAccc                                >  2:250958/1‑148 (MQ=255)                                                                                                                     aaacacacAGACTCAGACATATCCACTC‑TAGACCGGGTCTATGAGGGGATATGTAGGTTATCAGCGTATCAAGCCCCCCAGACCCTCGAGCAATCGCGGCAAAGACCCCTGACTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATgc                            <  4:189782/142‑1 (MQ=255)                                                                                                                          aCCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTgg                       <  8:41438/149‑1 (MQ=255)                                                                                                                          aCCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTgg                       <  2:22365/149‑1 (MQ=255)                                                                                                                               aaTCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTc                  <  6:139768/149‑1 (MQ=255)                                                                                                                                aTCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGAGCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTcc                 <  7:19712/149‑1 (MQ=255)                                                                                                                                 tCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCCTCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCt                >  6:223174/1‑149 (MQ=255)                                                                                                                                    gACATATCCACTCAAAGACCCGGTC‑TAGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGGCCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCCTCCCCGCCCTGCCCGCCTCCCCCAAGCGCTCGTCGTCCTGCg             >  4:176736/1‑149 (MQ=25)                                                                                                                                     aCATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCgg            >  6:323774/1‑149 (MQ=255)                                                                                                                                     aCATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCgg            <  1:275470/149‑1 (MQ=255)                                                                                                                                       atatCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGCTTGGCCCGCATCACCGCCCTGCCGGCCTCACCCATGCGCTGGGCGTCCTGCgg            >  2:10994/1‑147 (MQ=255)                                                                                                                                              ctc‑tAGTCCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTccac   <  5:236979/149‑1 (MQ=255)                                                                                                                                                  tAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGcc                                               >  5:205188/1‑102 (MQ=255)                                                                                                                                                  tAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGcc                                               <  6:205188/102‑1 (MQ=255)                                                                                                                                                  tAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTccacc  <  5:323774/147‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                   TCCCACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCACC  >  NC_002947/5608150‑5608440

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: ‑