Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,608,300	G→C	12.5%	intergenic (‑162/+26)	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	5,608,300	0	G	C	12.5%	129.0 / 10.0	48	intergenic (‑162/+26)	cyaB/waaA	cyclolysin secretion/processing ATP‑binding protein CyaB/3‑deoxy‑D‑manno‑octulosonic acid transferase
Reads supporting (aligned to +/- strand):  ref base G (18/24);  new base C (3/3);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.07e-01

CACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCACCAGGC  >  NC_002947/5608153‑5608444                                                                                                                                                     |                                                                                                                                                  cacaAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCgg                                                                                                                                                  <  5:132718/149‑1 (MQ=255) cacaAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCgg                                                                                                                                                  <  7:237501/149‑1 (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                                                                                                                               <  5:146872/116‑1 (MQ=37)                                                     tAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTCAAAGACCCGGTC‑TAGAGTGGATATGTc                                                                                                                               >  6:146872/1‑116 (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                                                                             >  7:41438/1‑149 (MQ=255)                                                                      gCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGc                                                                             >  1:22365/1‑149 (MQ=255)                                                                             aTCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGa                                                                      <  3:108141/149‑1 (MQ=255)                                                                             aTCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGa                                                                      <  4:147174/149‑1 (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‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCAc                                      <  7:37576/148‑1 (MQ=255)                                                                                                               aataaataACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCAccc                                    >  2:250958/1‑148 (MQ=255)                                                                                                                  aaacacacAGACTCAGACATATCCACTC‑TAGACCGGGTCTATGAGGGGATATGTAGGTTATCAGCGTATCAAGCCCCCCAGACCCTCGAGCAATCGCGGCAAAGACCCCTGACTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATgc                                <  4:189782/142‑1 (MQ=255)                                                                                                                       aCCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTgg                           <  2:22365/149‑1 (MQ=255)                                                                                                                       aCCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTgg                           <  8:41438/149‑1 (MQ=255)                                                                                                                            aaTCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTc                      <  6:139768/149‑1 (MQ=255)                                                                                                                             aTCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGAGCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTcc                     <  7:19712/149‑1 (MQ=255)                                                                                                                              tCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCCTC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCt                    >  6:223174/1‑149 (MQ=255)                                                                                                                                 gACATATCCACTCAAAGACCCGGTC‑TAGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGGCCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCCTC‑CCCGCCCTGCCCGCCTCCCCCAAGCGCTCGTCGTCCTGCg                 >  4:176736/1‑149 (MQ=25)                                                                                                                                  aCATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCgg                >  6:323774/1‑149 (MQ=255)                                                                                                                                  aCATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCgg                <  1:275470/149‑1 (MQ=255)                                                                                                                                    atatCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGCTTGGCCCGCATC‑ACCGCCCTGCCGGCCTCACCCATGCGCTGGGCGTCCTGCgg                >  2:10994/1‑147 (MQ=255)                                                                                                                                           ctc‑tAGTCCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTccac       <  5:236979/149‑1 (MQ=255)                                                                                                                                               tAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGcc                                                   <  6:205188/102‑1 (MQ=255)                                                                                                                                               tAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGcc                                                   >  5:205188/1‑102 (MQ=255)                                                                                                                                               tAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTccacc      <  5:323774/147‑1 (MQ=255)                                                                                                                                                 gACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGGAAAGCCCCCTGATTGGCCACCATC‑ACCGCCCTCCCCGACTCCCCCATGCGCTGGGCGTCCTGCGGCAGTTccaccacac  >  5:108929/1‑146 (MQ=255)                                                                                                                                                 gACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATCTTCCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCACCAgg   <  1:250958/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  CACAAGCTTCCGACGCAAGCGTGTGACACTTCTGACTTTTAAAGTCTATTCGTAGGAAGTTTCCTAACGGCGAGAAATCCAGTGTAGGAAGTTACAACTTACGCCGTAGGAATAAATAACCAGAATCAGACATATCCACTC‑TAGACCGGGTCTTTGAGTGGATATGTCGGTTATCAGCGGATCAAGGCCCCCAGACCCTCGAGCAATCGCTGCAAAGCCCCCTGATTGGCCCGCATC‑ACCGCCCTGCCCGCCTCACCCATGCGCTGGGCGTCCTGCGGCAGTTCCACCAGGC  >  NC_002947/5608153‑5608444

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: ‑