Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,239,889	T→C	13.0%	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	13.0%	108.4 / 8.5	49	P142P (CCA→CCG)	ldh	leucine dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (19/22);  new base C (3/3);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.04e-01

CCACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTCGAA  >  NC_002947/5239747‑5240035                                                                                                                                               |                                                                                                                                                    ccACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCAGGACCGCTACCCGCAAGCCTCTCCGGGCATCGCTGCCCAGCCCGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCACATGCGGCGAt                                                                                                                                               <  2:226529/149‑1 (MQ=255)   aCCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATgg                                                                                                                                             <  5:289971/149‑1 (MQ=255)   aCCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATgg                                                                                                                                             >  8:58233/1‑149 (MQ=255)    ccGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGACAAACCCCTGGACCGCTACCCGCAAGCCTCTAAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGAGATggg                                                                                                                                            >  5:236300/1‑149 (MQ=255)          gCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGccc                                                                                                                                      >  4:103350/1‑149 (MQ=255)           cAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGccc                                                                                                                                      <  6:349773/148‑1 (MQ=255)                      ccAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGt                                                                                                                                           <  7:102642/132‑1 (MQ=255)                      ccAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGt                                                                                                                                           >  8:102642/1‑132 (MQ=255)                      ccAAGGCATAACCAACATTGCCCACCCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAgtggtg                                                                                                                          <  6:250813/149‑1 (MQ=255)                       aaGGGAATAACCATCATTGCCAAACCCATCGAGCGCTACCCGATAGCCTTGCAGGTCTTCGCTGCCCTGCTTTAACGTGGTTGTGGCACGTATGCCGGCTAACACCCCCTTCGCCGATTGTGGCGATGGGTCGCCCGATGCAgtggt                                                                                                                           <  6:236300/146‑1 (MQ=255)                             aTAACCAACATTGCCCAACCCCTCTACCTCTACCCTCAAGCCTCTCAGGTCATCGCTGCCAAGCCGTAACGTGTTTGTGGCACGTATGCCCGCTAACACCCCCATCCCCGCATGTGGGTATGGGTCGCCCGATGCAGTGGTGCTGGTCa                                                                                                                   <  4:347039/149‑1 (MQ=255)                                aCCAACATTGCCCAACCCCTGGACCGCCACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAgtg                                                                                                                             >  8:184610/1‑136 (MQ=255)                                aCCAACATTGCCCAACCCCTGGACCGCCACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAgtg                                                                                                                             <  7:184610/136‑1 (MQ=255)                                   aaCATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑Agg                                                                                                            >  8:192626/1‑149 (MQ=255)                                     cATTCCCCACCCCCTGGACCGCTACCCCCAAGCCTCTCAGGTCAGCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCCAACACCCCCAGCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGc                                                                                                          <  6:54822/149‑1 (MQ=255)                                       ttGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGt                                                                                                        <  7:283393/149‑1 (MQ=255)                                          cccAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAgtggtg                                                                                                                          <  6:317094/129‑1 (MQ=255)                                             aaCCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAg                                                                                                                               <  7:101104/121‑1 (MQ=255)                                             aaCCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAg                                                                                                                               >  8:101104/1‑121 (MQ=255)                                               ccccTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTggg                                                                                                >  2:197580/1‑149 (MQ=255)                                                     gACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATg                                                                                           <  7:58233/148‑1 (MQ=255)                                                       ccGCTCCCCGCAAGCCTCTCCGGTCAGCGCTGCCCCGCCGCAACGAGGTTGTGGCACGTATGCCCGCCAACACCCCCATCGCCGCATGGGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAg                                                                                        <  1:150521/149‑1 (MQ=255)                                                           tACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCa                                                                                    >  3:248733/1‑149 (MQ=255)                                                             cccGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGTCAGGGCGTGCTGTGGGCAATGCAGTCCAt                                                                                   <  1:197580/149‑1 (MQ=255)                                                             cccGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTc                                                                                      <  2:10441/145‑1 (MQ=255)                                                             cccGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTc                                                                                      >  1:10441/1‑145 (MQ=255)                                                             cccGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATg                                                                                  <  3:103350/149‑1 (MQ=255)                                                             cccGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATg                                                                                  >  2:239603/1‑149 (MQ=255)                                                             cccGCAAGCCTCTCAGGTAATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGGGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCAt                                                                                   <  2:303075/148‑1 (MQ=255)                                                                gCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTc                                                                                >  2:106632/1‑148 (MQ=255)                                                                           aGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAg                                                                      <  1:239603/147‑1 (MQ=255)                                                                                aTCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCa                                                                >  4:250671/1‑148 (MQ=255)                                                                                aTCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCa                                                                <  3:250671/148‑1 (MQ=255)                                                                                       cccAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCAc                                                        <  7:192626/149‑1 (MQ=255)                                                                                              ggAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCgatg                                                 <  1:106632/149‑1 (MQ=255)                                                                                                            gCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATg                                   >  7:263174/1‑149 (MQ=255)                                                                                                                gTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAg                               <  8:263174/149‑1 (MQ=255)                                                                                                                     cccGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATc                          >  2:99600/1‑149 (MQ=255)                                                                                                                                ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGa                        <  2:54947/140‑1 (MQ=255)                                                                                                                                ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGa                        >  1:54947/1‑140 (MQ=255)                                                                                                                                ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGc               >  5:47284/1‑149 (MQ=255)                                                                                                                                ccccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACGGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGAGGAAGCGGc               >  5:52484/1‑149 (MQ=255)                                                                                                                                 cccATCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCa                                                                >  6:303990/1‑99 (MQ=255)                                                                                                                                 cccATCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCa                                                                <  5:303990/99‑1 (MQ=255)                                                                                                                                  ccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGaa                    >  2:39554/1‑142 (MQ=255)                                                                                                                                  ccATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGaa                    <  1:39554/142‑1 (MQ=255)                                                                                                                                  ccATCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGaa                                            >  6:133993/1‑118 (MQ=255)                                                                                                                                  ccATCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGaa                                            <  5:133993/118‑1 (MQ=255)                                                                                                                                  ccATCGCCACATGCGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGcc              >  5:352186/1‑148 (MQ=255)                                                                                                                                               tgGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTCGaa  >  7:88656/1‑147 (MQ=255)                                                                                                                                               |                                                                                                                                                    CCACCGCATGCAATTGCTCCGCCAGGGCATAACCAACATTGCCCAACCCCTGGACCGCTACCCGCAAGCCTCTCAGGTCATCGCTGCCCAGCCGGAACGAGGTTGTGGCACGTATGCCCGCGAACACCCCCATCGCCGCATGTGGCGATGGGTCGCCCGATGCAGTGGTGCTGGTCACGT‑AGGGCGTGCTGTGGGCAATGCAGTCCATGTCCAAGGTCGAGGTGCCACTGTCCACGGCGATGATGAAGCGCCCATGCAAGGTATCGATGAAGCGGCCAAAGGCCTCGAA  >  NC_002947/5239747‑5240035

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: ‑