Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,549,606	T→A	10.6%	intergenic (+19/‑153)	PP_t47 → / → PP_4881	tRNA‑Leu/iron ABC transporter substrate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,549,606	0	T	A	10.6%	125.6 / 5.6	47	intergenic (+19/‑153)	PP_t47/PP_4881	tRNA‑Leu/iron ABC transporter substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (21/21);  new base A (3/2);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01

AAAGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAGGAAG  >  NC_002947/5549459‑5549751                                                                                                                                                    |                                                                                                                                                   aaaGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTg                                                                                                                                                   <  4:2895/149‑1 (MQ=255)  aaGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTg                                                                                                                                                   <  8:126490/148‑1 (MQ=255)  aaGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGc                                                                                                                                                  <  4:3733/149‑1 (MQ=255)    gCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTa                                                                                                                                                <  8:248929/149‑1 (MQ=255)     cGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAg                                                                                                                                               >  7:269322/1‑149 (MQ=255)               tCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGCTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTCGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGttttat                                                                                                                                     >  3:131671/1‑147 (MQ=255)                 gCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTc                                                                                                                                    <  2:300544/148‑1 (MQ=255)                             tgatgTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGAttt                                                                                                                       <  7:104379/149‑1 (MQ=255)                             tgatgTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACAATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGAtt                                                                                                                        >  8:104379/1‑148 (MQ=255)                                tgTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTGTTTTCGTGCCTGCGATTTAtg                                                                                                                    >  8:127637/1‑149 (MQ=255)                                  tAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTAtgtg                                                                                                                  >  5:298967/1‑149 (MQ=255)                                                 gttggggAATTTGGAGAACCGCTGTTTTCAGGTAACACTTACCCCAAGCTCGTGGAAGTTGCAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCtt                                                                                                   <  6:179699/144‑1 (MQ=25)                                                    gCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCGGCGTCCCCCCCTAGCa                                                                                                >  6:39584/1‑149 (MQ=255)                                                       gAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCAAGCTAGTggg                                                                                                                                           <  1:186814/103‑1 (MQ=255)                                                       gAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCAAGCTAGTggg                                                                                                                                           >  2:186814/1‑103 (MQ=255)                                                            ggTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACACACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGGCGCGTCCCCCCCTTGCACCAGGGTc                                                                                        >  4:33/1‑149 (MQ=25)                                                                gACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTTCGCCCTCCCCCCCTTGCACCAATGTCTG‑Ac                                                                                   >  2:253124/1‑149 (MQ=255)                                                                gACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑Ac                                                                                   >  4:95396/1‑149 (MQ=255)                                                                gACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCATTCAACATGGTcatac                                                                                    >  4:42172/1‑145 (MQ=255)                                                                      cTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGaa                                                                             <  6:298967/149‑1 (MQ=255)                                                                       tGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTTCCCCCTCCCCCCCGTGCACCATGGTCTG‑CCAATGAAt                                                                            >  4:99495/1‑149 (MQ=255)                                                                          tttCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTGTG‑ACCATGAAGTtc                                                                         >  3:230171/1‑149 (MQ=255)                                                                              aGGTATCAGTGACCGCAAGTTCGTGGAAGTTCGTGTCTTCTCCTGGGCACCATAGAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCGTGCGATTTATGTGCCCCCTCGCACCCTTGCTCCATGGTCTG‑ACCATGAATTTCTCg                                                                      <  4:131671/148‑1 (MQ=38)                                                                                gTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTg                                                                                                                                 <  2:2075/88‑1 (MQ=255)                                                                                gTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTg                                                                                                                                 >  1:2075/1‑88 (MQ=255)                                                                                   tCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTT‑ACCATGAATTTCTCGTCacac                                                                <  1:314882/149‑1 (MQ=255)                                                                                     aGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGGCCCCTCCCCCCCTTGCACCAAGGTCTGCACCA‑GAATTTCACGTCACACgg                                                              >  2:1418/1‑149 (MQ=38)                                                                                      gTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTCAACCATGGTCTG‑ACCGTGAAGTTGTCGTGAAACGGc                                                             >  8:288454/1‑149 (MQ=38)                                                                                         aCCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCGTGGCCCATGGTGGG‑GCCATGAATTTCGCGTGCCACGGCCAc                                                          >  4:302020/1‑149 (MQ=38)                                                                                              atgttCGTGGAAGTTCGAGTCTTCTCCTGTGCACCATACAAATACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTgag                                                     <  7:45353/145‑1 (MQ=255)                                                                                                                   ttctCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTAGCACCATGGTCTG‑ACCATGCATTTCTCGGAAAACGGCCACGAGAGAAACAATTTCGATAACCAtgt                                >  8:217756/1‑147 (MQ=255)                                                                                                                      tcCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACAATGAATTTGTCGTCACCCGGCCACTTGAGAAAGAATTTGGTTTACCATTGttt                             >  2:197557/1‑149 (MQ=255)                                                                                                                        cTGTGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTcc                           <  7:288454/149‑1 (MQ=255)                                                                                                                        cTGGGCACCATACAAAAACCCACTAGCTTTCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGtt                              <  3:302020/146‑1 (MQ=255)                                                                                                                        cTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGtt                              <  1:224404/146‑1 (MQ=255)                                                                                                                             cACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATTGTCTG‑ACCATTAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAata                      <  7:217756/149‑1 (MQ=255)                                                                                                                              aCCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAatat                     <  8:269322/149‑1 (MQ=255)                                                                                                                              aCCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAatat                     <  1:197557/149‑1 (MQ=255)                                                                                                                                cATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGaa                                                   <  7:91738/117‑1 (MQ=255)                                                                                                                                   gaaaaaaCCCACTAGCAAGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTAACACGTCAACTTGAGAAACAATTTAGTTTACCATTGTTTCCAAATATGTAg                 >  6:178389/3‑148 (MQ=255)                                                                                                                                           ccACTAGCAAGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGc         >  2:152922/1‑148 (MQ=255)                                                                                                                                            cACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTTACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGa       <  1:253124/149‑1 (MQ=255)                                                                                                                                            cACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGa       <  3:95396/149‑1 (MQ=255)                                                                                                                                              cTAGCAAGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAgg     <  5:178389/149‑1 (MQ=255)                                                                                                                                               tAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCT‑CCCCCCTTGCACCATGGTCTG‑ACCATGAATTTATCATCAAACGGCCACTTGAGAAACAATTTCGTTTACCAATGTTTAGATATATGTTCGCGAAAGCCAGGaa   >  7:235110/1‑149 (MQ=255)                                                                                                                                                aGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGGCTG‑ACCATGAATTTCTCGTCACCCGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTGCAAAGATGTAGCAGTAAGCGAgg     >  2:101998/1‑147 (MQ=255)                                                                                                                                                 gCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCGCCCCCCCTTGCACCCTGGTCTG‑ACCAAGAATTTATCGTAACACGGCCCCTTGAGAAACAATTTAGTTTAACATTGTTTGCAAATATGTAGACGTAAGAGAGGAAg  >  8:33185/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                   AAAGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTG‑ACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAGGAAG  >  NC_002947/5549459‑5549751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑