Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,900,088	T→C	7.5%	intergenic (+49/‑449)	PP_4308 → / → PP_4309	AsnC family transcriptional regulator/NCS1 family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,900,088	0	T	C	7.5%	150.3 / 3.0	53	intergenic (+49/‑449)	PP_4308/PP_4309	AsnC family transcriptional regulator/NCS1 family transporter
Reads supporting (aligned to +/- strand):  ref base T (26/23);  new base C (2/2);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.29e-01

CCTGCTCGACCTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGATCAACTAATCAATCTTTCAAAAAT  >  NC_002947/4899949‑4900235                                                                                                                                            |                                                                                                                                                     ccTGCTCGACCTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGaa                                                                                                                                               >  1:189560/1‑147 (MQ=255) ccTGCTCGACCTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGaa                                                                                                                                               >  6:165054/1‑147 (MQ=255)        gACCTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGACTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGa                                                                                                                                        <  3:65448/147‑1 (MQ=255)         aCCTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTAGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTa                                                                                                                                    >  5:75598/1‑149 (MQ=255)           cTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACGCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCAAGTAAAGGAAAAGATGA‑GTagt                                                                                                                                  >  7:264302/1‑147 (MQ=255)                        tGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTa                                                                                                                           <  8:218368/143‑1 (MQ=255)                        tGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTa                                                                                                                           >  7:218368/1‑143 (MQ=255)                             gagaCCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACg                                                                                                                 >  2:170767/1‑148 (MQ=255)                              agaCCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGt                                                                                                                >  4:107380/1‑148 (MQ=255)                                         gcgATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTAAACAAAAACGTAACCATAgtggc                                                                                                    >  8:288990/1‑145 (MQ=255)                                               atcaAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCAtttt                                                                                              >  2:83602/1‑149 (MQ=255)                                                  aagaagACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTtgt                                                                                           <  2:189560/149‑1 (MQ=255)                                                  aagaagACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTtgt                                                                                           <  5:197249/149‑1 (MQ=255)                                                  aagaagACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTtgt                                                                                           <  6:325757/149‑1 (MQ=255)                                                  aagaagACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCAGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTtgt                                                                                           <  6:75598/149‑1 (MQ=255)                                                    gaagaCCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTtgtgt                                                                                         >  3:141087/1‑149 (MQ=255)                                                       gaCCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAACAGGCCAGTACAGGAAAAACTGAGGTATTTTTTTTACACAAAAACGTAACCATAGGTGCCATTTTtgtgtg                                                                                        >  1:102252/1‑148 (MQ=39)                                                          cccGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTCA‑GAATTTTTTTTAAACAAAAAAGTAACCCTAGGTTCCATTTTTTTTTTCACtt                                                                                   >  1:260775/1‑149 (MQ=38)                                                            cGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTttc                                                                                 <  7:103103/149‑1 (MQ=255)                                                                 aaGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAg                                                                            <  1:170767/149‑1 (MQ=255)                                                                 aaGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAg                                                                            >  2:96361/1‑149 (MQ=255)                                                                    cggcggTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTgg                                                                         <  1:83602/149‑1 (MQ=255)                                                                      gcggTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGgcg                                                                       <  4:141087/149‑1 (MQ=255)                                                                              cgccAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAAtt                                                               <  5:122042/149‑1 (MQ=255)                                                                              caccAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAAtt                                                               >  8:20510/3‑149 (MQ=255)                                                                                  aaTGGATTGATTGGCTCCTGTGCTTGCCTCTTCGCAGGCGTGCCCGCGAAGATGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCttt                                                           <  7:7860/149‑1 (MQ=255)                                                                                   aTGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCTCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTa                                                          <  6:201802/149‑1 (MQ=255)                                                                                       attgattgGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCAtttt                                                                                              <  1:183140/109‑1 (MQ=255)                                                                                       attgattgGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCAtttt                                                                                              >  2:183140/1‑109 (MQ=255)                                                                                            ttgGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTc                                                 >  4:246396/1‑149 (MQ=255)                                                                                              ggCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTcc                                                <  5:165054/148‑1 (MQ=255)                                                                                               gCTCCTGTGCTGGCCTGTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACATGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCa                                               <  7:288990/148‑1 (MQ=255)                                                                                                     gtgCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCTTAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTa                                        >  4:300602/1‑149 (MQ=255)                                                                                                       gCTGGCCTCTTCGCAGGCGTGCCCTCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGtt                                                           <  1:232221/128‑1 (MQ=255)                                                                                                       gCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGtt                                                           >  2:232221/1‑128 (MQ=255)                                                                                                           gCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTAtttt                                    <  7:20510/147‑1 (MQ=255)                                                                                                            ccTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCTTAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGAc                                 <  3:300602/149‑1 (MQ=255)                                                                                                             ctctTCGCGGGCACGCCTGCGAAGAGGCCAGCACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTa                                                          <  6:247527/123‑1 (MQ=38)                                                                                                             ctctTCGCGGGCACGCCTGCGAAGAGGCCAGCACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTa                                                          >  5:247527/1‑123 (MQ=38)                                                                                                             ctctTCGCAGGCGTGTCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGt                                                            >  3:293884/1‑121 (MQ=255)                                                                                                             ctctTCGCAGGCGTGTCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGt                                                            <  4:293884/121‑1 (MQ=255)                                                                                                             ctctTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGAc                                 >  7:225893/1‑148 (MQ=255)                                                                                                              tctTCGCGGGCACGCCTGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTATTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGAcc                                >  5:210018/1‑148 (MQ=255)                                                                                                              tctTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGAcc                                >  7:233890/1‑148 (MQ=255)                                                                                                                ttCGCGGGCACGCCTGCGAAGAGGCCAGCACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCaa                                                                 >  6:22055/1‑113 (MQ=38)                                                                                                                ttCGCGGGCACGCCTGCGAAGAGGCCAGCACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCaa                                                                 <  5:22055/113‑1 (MQ=38)                                                                                                                   gCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGa                          <  3:246396/149‑1 (MQ=255)                                                                                                                       gCGTGCCCGCGAAGAGGCCAGTGCAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCAATTTTTGTGTGCACTTTCTTCAGTGGCGccc                                                                    >  7:199526/1‑103 (MQ=255)                                                                                                                        cGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGATCAAc                     <  2:102252/149‑1 (MQ=255)                                                                                                                             ccGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGATCAACTaag                 >  5:278999/1‑147 (MQ=255)                                                                                                                                 gAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGATCAACTaatcaatc            >  6:171538/1‑149 (MQ=255)                                                                                                                                           gTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCGATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGAGCAAATGATCAACTTATCAATCTTTCaaaatt  >  2:213206/1‑147 (MQ=255)                                                                                                                                           gTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGATCAACTAATCAATCTTTCAAAAAt  <  6:278999/149‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                     CCTGCTCGACCTCATGAATGTGCTGGCCGAGACCAATACCGCGATCATCAAGAAGACCCCGGTCAAGCGGCGGTTGCCGCCAATGGATTGATTGGCTCCTGTGCTGGCCTCTTCGCAGGCGTGCCCGCGAAGAGGCCAGTACAGGAAAAGCTGA‑GTATTTTTTGTACACAAAAACGTAACCATAGGTGCCATTTTTGTGTGCACTTTCTTCAGTGGCGCCCCAATTCGTTACACACTTTCCACCCTCTATTTTGACCAAATGATCAACTAATCAATCTTTCAAAAAT  >  NC_002947/4899949‑4900235

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: ‑