Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,549,605	T→A	9.5%	intergenic (+18/‑154)	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	5,549,605	0	T	A	9.5%	109.7 / 3.2	42	intergenic (+18/‑154)	PP_t47/PP_4881	tRNA‑Leu/iron ABC transporter substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (20/18);  new base A (2/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.82e-01

GAAAGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAGGAA  >  NC_002947/5549458‑5549750                                                                                                                                                    |                                                                                                                                                  gAAAGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCtt                                                                                                                                                  >  8:90331/1‑149 (MQ=255) gAAAGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCtt                                                                                                                                                  >  8:258032/1‑149 (MQ=255)             tAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGttt                                                                                                                                      >  6:320802/1‑149 (MQ=255)               gTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCAAGCTAGTGGGttttt                                                                                                                                    <  2:103290/149‑1 (MQ=255)                tCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGttttt                                                                                                                                    >  6:38427/1‑148 (MQ=255)                   ccTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCtt                                                                                                                                >  2:119024/1‑149 (MQ=255)                         gCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGc                                                                                                                          >  4:162012/1‑149 (MQ=255)                             atgatgTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTACCTTGCTAGTGGGTTATTTCTTGCCTGCGaat                                                                                                                      >  7:355719/1‑147 (MQ=255)                                atgTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTAt                                                                                                                   <  1:119024/149‑1 (MQ=255)                                 tgTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTAtg                                                                                                                  >  5:6191/1‑149 (MQ=255)                                  gTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTAtgt                                                                                                                 >  5:142520/1‑149 (MQ=255)                                            gCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCGCGCTccc                                                                                                       >  5:355591/1‑149 (MQ=255)                                             cccAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCAAGCTAGTGGGtttttgta                                                                                                                                 <  1:175247/122‑4 (MQ=255)                                             cccAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCAAGCTAGTGGGtttttgta                                                                                                                                 >  2:175247/1‑119 (MQ=255)                                                     gcgcAATCGGTCGCCGCGCGGGTTTCAGGCATCAGTGACCGCAAGGGCGTGGCAGTTCGAGGCCTCTCCAGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGCTTTTTTCTTGCCTGCGATTTATGTCCCCCCTCCCCCCCTTGCa                                                                                              <  8:355719/149‑1 (MQ=255)                                                      cGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCAc                                                                                             <  5:38427/149‑1 (MQ=255)                                                           ttGGTAGACGCGCTGGTTTCATGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATgg                                                                                        <  1:5913/149‑1 (MQ=255)                                                                 gACGCGCTGGTTTCAGGTATCAGTGACCGCGAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGAc                                                                                  <  1:182605/149‑1 (MQ=255)                                                                    gcgcTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGc                                                                                                                                                <  5:119784/84‑1 (MQ=255)                                                                    gcgcTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGc                                                                                                                                                >  6:119784/1‑84 (MQ=255)                                                                      gcTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTATTTTCTTGCCTGCCAGTTATGTGCCCCCTGCCCCCCTTGCCCCATGGTCTGACCATg                                                                              >  4:356219/1‑148 (MQ=37)                                                                          gTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAAtt                                                                          <  4:262474/148‑1 (MQ=255)                                                                                      aGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACgg                                                             <  7:90331/149‑1 (MQ=255)                                                                                      aGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACgg                                                             <  7:258032/149‑1 (MQ=255)                                                                                      aGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACg                                                              <  5:320802/148‑1 (MQ=255)                                                                                            cGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACtt                                                       <  7:198564/149‑1 (MQ=255)                                                                                                    cGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCGGGGCCCATGGTCGGGCGATGAATTTGGGGTCACACGGGCACTTGAGaacc                                                >  7:78773/1‑146 (MQ=255)                                                                                                      tGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGGCCCCTCCCCCCCGTGGACCATGGTCTGACCATGAAATTCTAGTCAAACGGCCACATGaaaagatgg                                             >  4:174628/1‑144 (MQ=255)                                                                                                      tGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTgag                                                    <  3:174628/142‑1 (MQ=255)                                                                                                           gTTCGAGTCTTCTCCTGGACACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCGTGCACCATGGTCTGACCATGAATTTCACGTCACACGGCCACTTGACAAACAATTTAGt                                        >  3:75680/1‑149 (MQ=255)                                                                                                             tCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATg                                                                              <  7:269579/109‑1 (MQ=255)                                                                                                             tCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCAAGGTCGGACAATg                                                                              >  8:269579/1‑109 (MQ=255)                                                                                                                       tcCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCGCCTCCCCCGCGTGCACCAGGGGCTGACAAGGAATGTCTCGTCACCCGGCCGCTGGCGAAACAAGTTGGTTTACCATAGttg                            >  6:102916/1‑148 (MQ=255)                                                                                                                         cTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTcc                          <  3:162012/149‑1 (MQ=255)                                                                                                                            ggCACCATACAAAAACCCACTAGCTTGCTAGTGTGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCaaa                       <  5:224753/149‑1 (MQ=255)                                                                                                                            ggCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCaaa                       <  2:302520/149‑1 (MQ=255)                                                                                                                               ccatctcAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCGCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAata                     <  1:38494/142‑1 (MQ=255)                                                                                                                                  aTACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTGCAAATATg                   >  2:135464/1‑147 (MQ=255)                                                                                                                                         aaCCCACTAGCAAGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCGTGCACCATGGTCTGACCAAGAATTTCACGTCAAACGCGCACTTGAGACACAATATCCTTTACCATTGTTTCCAAAGATGTAGCCGt            >  2:287054/1‑147 (MQ=255)                                                                                                                                          aCCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCGCCCTCCCCCCCTGGCACCATGGTGTGACCATGAATTTCTGGTCACACGGCGACGTGAGAAACAATTTGGTTTTCCGTTGTTTCGAAAGATGTAGcaggtag         >  4:28475/1‑143 (MQ=255)                                                                                                                                            ccACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCGTGCCCCCCTTGCACCATGGTCTGCCCATGAATTTGTCGGAACAAGGCCACTTGAGAAACATTTTGGTTTACCATTGTTTCCAAATATGTTGACTTAAGCg       >  2:219444/1‑149 (MQ=255)                                                                                                                                              aCTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAg     >  2:11118/1‑149 (MQ=255)                                                                                                                                                tAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGGCCCCTCCCCCCCTTGCACCATGGTCTGGCCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTGGTTTACCATTTTTTCCATATATGTAGACGTAAGGGAggt   >  5:193700/1‑148 (MQ=255)                                                                                                                                                  gCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAGGaa  <  6:6191/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  GAAAGCGAACGATAGTCGCCTTCTGCAGATGATGTAAAGCTTTGCCCAGGTGGCGGAATTGGTAGACGCGCTGGTTTCAGGTATCAGTGACCGCAAGGTCGTGGAAGTTCGAGTCTTCTCCTGGGCACCATACAAAAACCCACTAGCTTGCTAGTGGGTTTTTTCTTGCCTGCGATTTATGTGCCCCCTCCCCCCCTTGCACCATGGTCTGACCATGAATTTCTCGTCACACGGCCACTTGAGAAACAATTTCGTTTACCATTGTTTCCAAATATGTAGCCGTAAGCGAGGAA  >  NC_002947/5549458‑5549750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑