Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,080,964	A→T	16.7%	intergenic (‑144/+19)	amaC ← / ← dpkA	D‑lysine aminotransferase/delta 1‑piperideine‑2‑carboxylate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,080,964	0	A	T	16.7%	96.7 / 13.0	42	intergenic (‑144/+19)	amaC/dpkA	D‑lysine aminotransferase/delta 1‑piperideine‑2‑carboxylate reductase
Reads supporting (aligned to +/- strand):  ref base A (21/14);  new base T (4/3);  total (25/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

GTGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCATGTGCT  >  NC_002947/4080824‑4081113                                                                                                                                             |                                                                                                                                                      gTGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGaa                                                                                                                                              >  2:913090/1‑150 (MQ=255)  tGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAg                                                                                                                                             <  1:727901/150‑1 (MQ=255)   gCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAgg                                                                                                                                            <  1:887840/150‑1 (MQ=255)    cAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAggg                                                                                                                                           <  2:326405/150‑1 (MQ=255)    cAGCTCCTTGGATCAGGACAGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAggg                                                                                                                                           <  2:778090/150‑1 (MQ=255)          cTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGcc                                                                                                                                        <  2:993804/147‑1 (MQ=255)          cTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGcc                                                                                                                                        >  1:993804/1‑147 (MQ=255)                tCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGcc                                                                                                                               >  1:1118596/1‑150 (MQ=255)                tCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACAGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGcc                                                                                                                               >  2:1051772/1‑150 (MQ=255)                tCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGACAATGCAACATTGCATGAACGGCCTGCAGGAGTTCTTGTGCGTGGTGGAACCCGCGAAGGGGCCAAATCAGcc                                                                                                                               >  1:519283/1‑150 (MQ=255)                         tACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGctc                                                                                                                      >  1:333359/1‑150 (MQ=255)                              aaaGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCa                                                                                                                 <  2:658591/150‑1 (MQ=255)                                      tgtTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGATCTTTCAGGCCTTTc                                                                                                         <  1:913090/150‑1 (MQ=255)                                            gCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTcc                                                                                                   >  2:989808/1‑150 (MQ=255)                                              aTACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCGTTCAACTCCTg                                                                                                 >  1:102083/1‑150 (MQ=255)                                               tACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGc                                                                                                <  1:1051772/150‑1 (MQ=255)                                                  ccGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATTACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCg                                                                                             <  1:492954/150‑1 (MQ=255)                                                                 aGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCAccccc                                                                              >  2:682650/1‑150 (MQ=255)                                                                          cACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCg                                                                     >  1:946611/1‑150 (MQ=255)                                                                          cACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCg                                                                     >  2:15077/1‑150 (MQ=255)                                                                                  tgCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTc                                                             >  2:992262/1‑150 (MQ=255)                                                                                  tgCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTc                                                             <  1:15077/150‑1 (MQ=255)                                                                                      aGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCgcgc                                                         <  1:992262/150‑1 (MQ=255)                                                                                                 gCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAgcg                                              >  2:1126728/1‑150 (MQ=255)                                                                                                                cGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGACACGCAGCCGTTTCAGGCCTTTCAACCCCTGCTCGCTCACCGCCACCCCCGCCTCCTCGGCCACCTCCCGCTCACGGTAGCGCCCCTCCCCCGGCAt                               >  2:214835/1‑150 (MQ=255)                                                                                                                 gggATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATg                              >  1:582938/1‑150 (MQ=255)                                                                                                                 gggATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATg                              >  1:582902/1‑150 (MQ=255)                                                                                                                    aTGAGGGCCGGCTTTTCCGCGGGTAAACTCGCGAAGGGGCCAAATCATCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATgcac                           <  1:588162/150‑3 (MQ=255)                                                                                                                     tGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAgg                                                                                                               >  2:905872/1‑65 (MQ=255)                                                                                                                     tGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAgg                                                                                                               <  1:905872/65‑1 (MQ=255)                                                                                                                         ggctggctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAg                      >  2:1103409/1‑150 (MQ=255)                                                                                                                            tggctTTTTCGCGGGTAAACCCGCGAAGGGGCAAAAACAGCACCGTAGCACTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGccc                   >  1:749785/1‑150 (MQ=255)                                                                                                                              gctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCAc                                                                                  <  1:850509/85‑1 (MQ=255)                                                                                                                              gctTTTTCGCGGATAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCAc                                                                                  >  2:850509/1‑85 (MQ=255)                                                                                                                                tttttCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCAcc               >  1:893623/1‑150 (MQ=255)                                                                                                                                cccttCGCGGGTTTACCCGCGAAAGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATgc                             >  1:357701/4‑136 (MQ=255)                                                                                                                                cccgtCGCGGGTTTACCCGCGAAAGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATgc                             <  2:357701/132‑1 (MQ=255)                                                                                                                                 ccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCa                                                                                   >  2:701129/3‑81 (MQ=38)                                                                                                                                 ccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCa                                                                                   >  2:281134/3‑81 (MQ=38)                                                                                                                                 ccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCa                                                                                   <  1:281134/79‑1 (MQ=38)                                                                                                                                 ccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCa                                                                                   <  1:701129/79‑1 (MQ=38)                                                                                                                                   ttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGcc            >  2:394525/1‑150 (MQ=255)                                                                                                                                             aaCCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCATGTGCt  >  2:181273/1‑150 (MQ=255)                                                                                                                                             |                                                                                                                                                      GTGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTATGCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCATGTGCT  >  NC_002947/4080824‑4081113

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑