Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,372,122	G→A	11.0%	intergenic (‑50/‑69)	csoR ← / → PP_2970	copper utilization transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,372,122	0	G	A	11.0%	139.5 / 6.4	55	intergenic (‑50/‑69)	csoR/PP_2970	copper utilization transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (27/21);  new base A (4/2);  total (31/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.71e-01

GACGATGCTGCGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGCACAC  >  NC_002947/3371980‑3372267                                                                                                                                               |                                                                                                                                                    gACGATGCTGCGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTgggg                                                                                                                                                   <  1:201099/145‑1 (MQ=255) gACGATGCTGCGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTgggg                                                                                                                                                   >  2:201099/1‑145 (MQ=255)    gATGCTGCGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGatat                                                                                                                                            <  8:75392/149‑1 (MQ=255)        ctgcGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGt                                                                                                                                         >  4:25150/1‑148 (MQ=255)        ctgcGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGt                                                                                                                                         <  5:287543/148‑1 (MQ=255)        ctgcGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGt                                                                                                                                         <  3:25150/148‑1 (MQ=255)                gTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAAc                                                                                                                                <  5:66112/149‑1 (MQ=255)                      cTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAc‑ccc                                                                                                                         >  7:182657/1‑149 (MQ=255)                            aCGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCtt                                                                                                                       <  8:110221/145‑1 (MQ=255)                            aCGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCtt                                                                                                                       >  7:110221/1‑145 (MQ=255)                                ttCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCACACCAACTAC‑CCCTTCCGaacaa                                                                                                               >  8:67236/1‑149 (MQ=255)                                  cAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGaacaac                                                                                                              >  2:52896/1‑148 (MQ=255)                                   aaCCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCa                                                                                                            >  1:294710/1‑149 (MQ=255)                                    aCCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCCCAGGGGGataggat                                                                                                                                         <  3:23833/120‑5 (MQ=255)                                    aCCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCCCAGGGGGataggat                                                                                                                                         >  4:23833/1‑116 (MQ=255)                                           gatgatATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCt                                                                                                     >  5:226731/1‑147 (MQ=255)                                            atgatATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAAc                                                                                                                                    >  7:758/1‑117 (MQ=255)                                            atgatATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTa                                                                                                   <  6:226731/148‑1 (MQ=255)                                              gatATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCATACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAgg                                                                                                 >  7:119943/1‑148 (MQ=255)                                               atatCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGc                                                                                                <  8:193524/148‑1 (MQ=255)                                                    gCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCaaa                                                                                          <  8:182657/149‑1 (MQ=255)                                                    gCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCaa                                                                                           <  2:294710/148‑1 (MQ=255)                                                      tATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCaa                                                                                           >  3:109036/1‑146 (MQ=255)                                                            tttGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAacac                                                                                  >  8:277330/1‑149 (MQ=255)                                                                 tGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACAt                                                                             >  7:216744/1‑149 (MQ=255)                                                                 tGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACAt                                                                             >  8:184344/1‑149 (MQ=255)                                                                 tGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACAt                                                                             <  2:22332/149‑1 (MQ=255)                                                                        ggCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAg                                                                       >  4:7914/1‑148 (MQ=255)                                                                        ggCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCAACC‑GCTTAGGCATCAAAAGAACCACGACATGATCAg                                                                       >  4:12591/1‑148 (MQ=255)                                                                           cGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAAc                                                                   >  4:113892/1‑149 (MQ=255)                                                                                 cGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCAt                                                              <  7:184344/148‑1 (MQ=255)                                                                                  gTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCCTTATTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCAt                                                              >  1:274436/1‑148 (MQ=255)                                                                                     aTCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGc                                                          >  3:193934/1‑148 (MQ=255)                                                                                            aTGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGTGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAg                                                    <  8:216744/147‑1 (MQ=255)                                                                                            aTGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAgg                                                   <  7:67236/148‑1 (MQ=255)                                                                                                        tcATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGTATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGccc                                       <  3:12591/148‑1 (MQ=255)                                                                                                        tcATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACAt                                                                             >  2:265265/1‑110 (MQ=255)                                                                                                        tcATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACAt                                                                             <  1:265265/110‑1 (MQ=255)                                                                                                          aTGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGccc                                       <  3:7914/146‑1 (MQ=255)                                                                                                              aTCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACAATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGctct                                >  8:223722/1‑149 (MQ=255)                                                                                                                      aTTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACAATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCt                        <  7:223722/149‑1 (MQ=255)                                                                                                                                 accatATCCCCCCCAGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAAcc                                                                  >  7:304796/5‑96 (MQ=255)                                                                                                                                 accatATCCCCCCCAGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAAcc                                                                  <  8:304796/92‑1 (MQ=255)                                                                                                                                  tCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCACCTTGATAGCCTggg            <  7:277330/149‑1 (MQ=255)                                                                                                                                  ccatATCCCCCCCAGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTggg            >  8:126146/4‑149 (MQ=255)                                                                                                                                   catATCCCCCCCAGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGc           >  2:251573/3‑149 (MQ=255)                                                                                                                                       tCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCggg       >  3:313059/1‑149 (MQ=255)                                                                                                                                       tCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCgg        <  4:109036/148‑1 (MQ=255)                                                                                                                                         ccccTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGca     >  4:155836/1‑149 (MQ=255)                                                                                                                                          cccTGGGGGGGATATGGTCAAACCAACTACGCCCTTCAGAACACCCATCC‑GCTTAGGCTTCAAAAGAAACACGACATGATCAGCAACCCAATAAGCACTAAGGTGATTTTTGCCCTTGATCTGGCCATCTTGATAGCCTGGGCCGGGca     >  1:197285/1‑149 (MQ=255)                                                                                                                                          cccTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGcac    >  5:255520/1‑149 (MQ=255)                                                                                                                                           ccTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCt               >  6:45431/1‑137 (MQ=255)                                                                                                                                           ccTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCt               <  5:45431/137‑1 (MQ=255)                                                                                                                                           ccTGGGGGGGATAT‑GTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGCacac  >  6:180668/1‑149 (MQ=255)                                                                                                                                           ccTGGGGGGGATAT‑GTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGCacac  >  2:260155/1‑149 (MQ=255)                                                                                                                                            cTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGCacac  <  6:255520/149‑1 (MQ=255)                                                                                                                                            cTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGCacac  <  3:113892/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                    GACGATGCTGCGCAGGTGGCCCTCCGCACGCTTCAACCTTTTGATGATATCGCTATGACTTTGGTGCTGATGGCCGTGTTCGTGATCGCTCATGCCTTGAGTCTCATGCATCGATGAATTACGCTCGCATCCTATCCCCCTGGGGGGGATATGGTCAAACCAACTAC‑CCCTTCAGAACAACCATCC‑GCTTAGGCATCAAAAGAAACACGACATGCTCAGCAACCCCATCAGCACTAAGGTGATTTTTGCCCTTGCTCTGGCCATCTTGATAGCCTGGGCCGGGCACAC  >  NC_002947/3371980‑3372267

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: ‑