Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,239,889	T→C	11.4%	P142P (CCA→CCG)	ldh ←	leucine dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,239,889	0	T	C	11.4%	134.0 / 8.2	54	P142P (CCA→CCG)	ldh	leucine dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (22/25);  new base C (3/3);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.90e-01

CGCGCCCACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTCGAACA  >  NC_002947/5239742‑5240037                                                                                                                                                    |                                                                                                                                                      cgcgCCCACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCAtgt                                                                                                                                                       <  2:352666/148‑1 (MQ=255) cccgcCCTCCGCATGACATTGCACCGCCCCGGCATAACCACACTCTCCCCACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCAGCGCTGCCCAGCCGGAACCAGGTTTTGGCACGTATGCCCGCGAACACCCCCATCGCCGCTtgtg                                                                                                                                                      <  4:296991/147‑1 (MQ=255)  gcgcCCACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTgg                                                                                                                                                     <  3:59302/149‑1 (MQ=255)      ccACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGAt                                                                                                                                                 <  7:23156/149‑1 (MQ=255)       cACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATg                                                                                                                                                <  6:245574/149‑1 (MQ=255)        aCCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATgg                                                                                                                                               >  2:172721/1‑149 (MQ=255)          cGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCACATGCGGCGATgggg                                                                                                                                             <  5:204229/149‑2 (MQ=255)                     gCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGACCACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATg                                                                                                                                    >  7:218513/1‑147 (MQ=255)                        ccGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAgtg                                                                                                                               <  6:182901/149‑1 (MQ=255)                           ccAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAgtggtg                                                                                                                            >  6:9934/1‑149 (MQ=255)                            cAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCACATGCGGCGATgg                                                                                                                                               <  3:72277/129‑1 (MQ=255)                            cAGGGCATAACCAACATTGCCCAACCCCAGGACCGCTACCCGCAAGCCTCTCACGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCACATGCGGCGATgg                                                                                                                                               >  4:72277/1‑129 (MQ=255)                                       cAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAg                                                                                                                >  7:281560/1‑149 (MQ=255)                                        aaCATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCGGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAgg                                                                                                               <  1:159104/149‑1 (MQ=255)                                        aaCATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAgg                                                                                                               <  8:84194/149‑1 (MQ=255)                                        aaCATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAgg                                                                                                               >  5:39557/1‑149 (MQ=255)                                                ccAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATG‑CCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCtgt                                                                                                      >  1:153503/1‑149 (MQ=255)                                                  aaCCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCtgtg                                                                                                     >  8:263792/1‑149 (MQ=255)                                                     cccTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTggg                                                                                                   >  7:296091/1‑148 (MQ=255)                                                      ccTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCCCGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGAGGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGc                                                                                                  >  5:95032/1‑148 (MQ=255)                                                         ggACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATg                                                                                              >  6:345517/1‑149 (MQ=255)                                                          gACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAAt                                                                                               <  2:224074/147‑1 (MQ=255)                                                          gACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATG‑CCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATg                                                                                              <  2:153503/147‑1 (MQ=255)                                                             cGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCAGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGt                                                                                          >  8:23355/1‑149 (MQ=255)                                                              gCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTc                                                                                         <  8:51838/149‑1 (MQ=255)                                                                     gCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTc                                                                                   >  4:177954/1‑148 (MQ=255)                                                                           ctctCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTc                                                                           <  5:345517/149‑1 (MQ=255)                                                                                aGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTcc                                                                                        >  7:342627/1‑132 (MQ=255)                                                                                aGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTcc                                                                                        <  8:342627/132‑1 (MQ=255)                                                                                aGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGa                                                                         <  7:23355/146‑1 (MQ=255)                                                                                aGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGt                                                                      <  5:299692/149‑1 (MQ=255)                                                                                aGGGCATCGCGGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGt                                                                      <  6:95032/149‑1 (MQ=255)                                                                                     aTCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCa                                                                  <  5:218425/148‑1 (MQ=255)                                                                                             ccAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACg                                                         >  2:289682/1‑149 (MQ=255)                                                                                             ccAGCCGGAACGAGGGTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACg                                                         <  5:9934/149‑1 (MQ=255)                                                                                                               tgGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGccc                                        <  7:263792/148‑1 (MQ=255)                                                                                                                 gCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATg                                     >  5:334929/1‑149 (MQ=255)                                                                                                                 gCACGTATGCCCGCGAACACCCCCATCGCCGCATATGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCa                                                                  >  1:329029/1‑120 (MQ=255)                                                                                                                     gTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAg                                 <  8:281560/149‑1 (MQ=255)                                                                                                                          cccGCGAACACCCCCATCGCCGCATGGGGGTATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATc                            <  1:172721/149‑1 (MQ=255)                                                                                                                           ccGCGTACACCCCCATCGCCGCTTGTGGCGATGAGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTGCATGTCCANAGGTCGAGGTGCCACTGTCCACGGCgatga                                                  <  1:32863/127‑1 (MQ=255)                                                                                                                           ccGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCGGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATc                            >  1:307891/1‑148 (MQ=255)                                                                                                                           ccGCGAACACCCCCATCGCCGCATGTGGCGATGAGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCgatga                                                  >  2:32863/1‑126 (MQ=255)                                                                                                                            cgcgAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGa                          <  6:39557/149‑1 (MQ=255)                                                                                                                             gcgAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGAt                         <  5:225359/149‑1 (MQ=255)                                                                                                                                   acCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCg                   >  8:186309/1‑149 (MQ=255)                                                                                                                                    cccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCgg                  <  7:186309/149‑1 (MQ=255)                                                                                                                                     ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCgat                                                    >  1:118543/1‑114 (MQ=255)                                                                                                                                     ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCgat                                                    <  2:114495/114‑1 (MQ=255)                                                                                                                                     ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCgat                                                    <  2:118543/114‑1 (MQ=255)                                                                                                                                     ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCgat                                                    >  1:114495/1‑114 (MQ=255)                                                                                                                                       ccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGcc                >  7:266525/1‑148 (MQ=255)                                                                                                                                       ccATCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGcc                >  1:300372/1‑148 (MQ=255)                                                                                                                                         aTCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATc                            <  8:101093/134‑1 (MQ=255)                                                                                                                                         aTCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATc                            >  7:101093/1‑134 (MQ=255)                                                                                                                                               gcATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTc       <  3:177954/149‑1 (MQ=255)                                                                                                                                                    tgGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTCGAACa  <  8:266525/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                      CGCGCCCACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTAGGGCGTGCTGTGGGCAATGCAGTCCATGTCCA‑AGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTCGAACA  >  NC_002947/5239742‑5240037

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: ‑