Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,497,001	T→C	12.1%	Q95R (CAA→CGA)	PP_1309 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,497,001	0	T	C	12.1%	83.2 / 3.0	33	Q95R (CAA→CGA)	PP_1309	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (12/17);  new base C (2/2);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

GTAGCTTTCGTCGAGCATGCCCGGCGAGTTAGGCGCTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCTGGTAGCTGTCGAAGC  >  NC_002947/1496862‑1497145                                                                                                                                            |                                                                                                                                                 gTAGCTTTCGTCGAGCATGCCCGGCGAGTTAGGCGCTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGAc                                                                                                                                        <  2:59684/150‑1 (MQ=255)      tttCGTCGAGCATGCCCGGCGAGTTAGGCGCTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCAt                                                                                                                                   >  1:501013/1‑150 (MQ=255)                 aTGCCCGGCGAGTTAGGAGTTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAgg                                                                                                                        <  1:438781/150‑1 (MQ=255)                           aGTTAGGCGCTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGGCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGgcgc                                                                                                              <  1:567413/150‑1 (MQ=255)                               aGGCGCTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTCGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTc                                                                                                          >  2:657200/1‑150 (MQ=255)                               aGGCGCTTTCGGCGCATACTCGCGCGGCACTTCGGCGGTGTCGTTGGGTGGAGTCAGCCGGTCACGCGGGCCTTGCGGGGCAGGGGAGTGCAGCGCAGCCAGCAGGCGTCGGCGGGGGACGGCGTGGAAGGCCAGGCTTTGAGCTCCTTc                                                                                                          >  2:261650/1‑150 (MQ=255)                                 gcgcTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAg                                                                                                        >  1:797798/1‑150 (MQ=255)                                         ggTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGa                                                                                                >  1:88609/1‑150 (MQ=255)                                               tAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGt                                                                                          <  2:501013/150‑1 (MQ=255)                                                  tCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATc                                                                                              >  2:576085/1‑143 (MQ=255)                                                  tCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATc                                                                                              <  1:576085/143‑1 (MQ=255)                                                    gcgcgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTc                                                                                     >  2:796297/1‑150 (MQ=255)                                                    gcgcgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTc                                                                                     >  1:713406/1‑150 (MQ=255)                                                     cgcgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTcc                                                                                    <  1:326467/150‑1 (MQ=255)                                                     cgcgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTCGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTcc                                                                                    <  1:657200/150‑1 (MQ=255)                                                     cgcgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTCGGCGGGTGACGTCATAGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTcc                                                                                    <  1:261650/150‑1 (MQ=255)                                                       cgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCt                                                                                                            <  1:57088/124‑1 (MQ=255)                                                       cgGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCt                                                                                                            >  2:57088/1‑124 (MQ=255)                                                         gCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGAt                                                                                <  2:713406/150‑1 (MQ=255)                                                          cACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATa                                                                               <  2:579847/150‑1 (MQ=255)                                                          cACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGAAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTATTCGTGCCTTCAGCCAGGTGATCCTGTACGTCCTGATa                                                                               <  1:786464/150‑1 (MQ=255)                                                             ttCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGct                                                                            >  2:102679/1‑150 (MQ=255)                                                                                 gggTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTa                                                                                         <  2:307783/117‑1 (MQ=255)                                                                                 gggTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTa                                                                                         >  1:307783/1‑117 (MQ=255)                                                                                         cGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCg                                                <  2:760960/150‑1 (MQ=255)                                                                                             cACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGc                                            <  1:102679/150‑1 (MQ=255)                                                                                                 cgGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGtt                                        <  2:88609/150‑1 (MQ=255)                                                                                                      cTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAAt                                   >  2:81346/1‑150 (MQ=255)                                                                                                                        gcagcgcagcCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCt                 >  1:415025/1‑150 (MQ=255)                                                                                                                          agcgcagcCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCCgg               <  1:796297/150‑1 (MQ=255)                                                                                                                                   agcagGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCTg                >  2:54211/1‑140 (MQ=255)                                                                                                                                   agcagGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCTg                <  1:54211/140‑1 (MQ=255)                                                                                                                                       ggCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCTGGTAGCTGTCGAAgc  <  2:5815/150‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                 GTAGCTTTCGTCGAGCATGCCCGGCGAGTTAGGCGCTTTCGGTGCATAGTCGCGCGGCACTTCGGCGGTGTCTTTAGGTGGGGTCAGGCGGTCACGCGGGCCTTGCGGTGCATCGGAGTGCAGCGCAGCCAGCAGGCGTTGGCGGGTGACGTCATCGAGGGCCAGGCTGTTGGCGCCTTCAGCCAGGTGATCCTGTACGTCCTGATAGCTCTGGGTCAGTTTCTTGACCAGCATGGCGGTGCTGTTGAAATGGGTGACCACTTCGTTCTGGTAGCTGTCGAAGC  >  NC_002947/1496862‑1497145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑