Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,608,293:1	+A	12.8%	intergenic (‑155/+33)	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	5,608,293	1	.	A	12.8%	162.8 / 22.0	47	intergenic (‑155/+33)	cyaB/waaA	cyclolysin secretion/processing ATP‑binding protein CyaB/3‑deoxy‑D‑manno‑octulosonic acid transferase
Reads supporting (aligned to +/- strand):  ref base . (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 = 9.05e-01

AAACGTCCCACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCAC  >  NC_002947/5608145‑5608439                                                                                                                                                      |                                                                                                                                                   aaaCGTCCCACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCActc                                                                                                                                                     <  8:231392/149‑1 (MQ=255)      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)                ttCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCActc                                                                                                                                                     <  8:9907/134‑1 (MQ=255)                ttCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCActc                                                                                                                                                     >  7:9907/1‑134 (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                                                                                                                                    <  2:160242/121‑1 (MQ=255)                                             ttttAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGa                                                                                                                                    >  1:160242/1‑121 (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                                                                                                                         <  5:146872/116‑1 (MQ=37)                                                             tAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTC‑TAGAGTGGATATGTc                                                                                                                         >  6:146872/1‑116 (MQ=37)                                                               ggAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAg                                                                                      <  4:106625/149‑1 (MQ=255)                                                                        cTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCttt                                                                                                                                      <  3:218772/92‑1 (MQ=255)                                                                        cTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCttt                                                                                                                                      >  4:218772/1‑92 (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                      <  2:22365/149‑1 (MQ=255)                                                                                                                               aCCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTgg                      <  8:41438/149‑1 (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           <  1:275470/149‑1 (MQ=255)                                                                                                                                          aCATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCgg           >  6:323774/1‑149 (MQ=255)                                                                                                                                            atatCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGCTTGGCCCGCATCACCGCCCTGCCGGCCTCACCCATGCGCTGGGCGTCCTGCgg           >  2:10994/1‑147 (MQ=255)                                                                                                                                                   ctc‑tAGTCCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTccac  <  5:236979/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                   AAACGTCCCACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCAC  >  NC_002947/5608145‑5608439

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: ‑