Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	3,951,161	A→T	intergenic (‑125/+70)	PP_3486 ← / ← PP_3487	cytochrome c/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,951,161	0	A	T	96.9%	100.5 / ‑5.7	32	intergenic (‑125/+70)	PP_3486/PP_3487	cytochrome c/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (23/8);  minor base G (1/0);  total (24/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

GGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTG  >  NC_002947/3951022‑3951292                                                                                                                                              |                                                                                                                                    ggTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGa                                                                                                                               <  7:286071/146‑1 (MQ=255)       aGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAgg                                                                                                                        <  1:34471/147‑1 (MQ=255)         ttGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCCGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCGTTCGCGACGCAAGGcc                                                                                                                      >  7:276126/1‑147 (MQ=255)                gccaAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGGGGGGGGGCACGGCGGGGCAGCAGCCCCGGCCGGGGGCGGGCCAGCGGCGCAGGAGGGGGGCGCGGCGC‑‑GGTCCGGTGGCGCCGCAGGGCCggggccc                                                                                                               >  6:276344/1‑141 (MQ=255)                gccaAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCCAAAGGGCTGCGCCCCCCCCCCCGCATTGGCCGCTCCAGCGCAGAAAGAGGGGAGCGCAGCCC‑‑GCTGCGTTCGCGGCGCCAGGGCGCACCca                                                                                                               >  5:349802/1‑147 (MQ=255)                   aaGCACGCAGGTAATCCATATCGCAAGCCCTGTGGGAGAGGCCGTTCGTACCCAAAGGGCAGCTCCGCAGCCACGGAATGAGCAGCAGCCGCGCCTAAAGAGGGGATGGCTGGGC‑‑GGTACTTTAGCGCCGCAAGGCCGCGcacaca                                                                                                             >  8:298365/1‑146 (MQ=255)                        cGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCATGAGTCGCGAAAGGGCTTCGCAGCAGCCCCGGAAGTGGCAGCACAAACGCAGAAAGAGGGGAGCCCGTCGC‑‑GCGACATTTGCGACCCCAGGGCGCTCACACaaaaca                                                                                                        >  6:188388/1‑144 (MQ=255)                                                       aggggCCTTGCGTCGCGAAAGGGCTGCGCAGCCGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGCGCGCTGCGC‑‑GCTCCTTTCGCGACGAAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGcc                                                                        <  8:276126/144‑1 (MQ=38)                                                             cTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATg                                                                    >  3:107440/1‑145 (MQ=255)                                                              ttGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATa                                                                 >  6:243588/1‑147 (MQ=255)                                                                 cGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTc                                                              >  1:181578/1‑147 (MQ=255)                                                                  gTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTACGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCa                                                             >  3:355412/1‑147 (MQ=255)                                                                   tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGCTGCCGCAGAGGCCAATTCCCCAGGCGGCCCATGATACTCac                                                            >  6:242492/1‑147 (MQ=255)                                                                      cgAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGGGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCacc                                                           >  1:117028/1‑147 (MQ=255)                                                                                     gcagcCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTgg                                          >  5:224977/1‑147 (MQ=255)                                                                                          cccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCaa                                     <  6:224977/147‑1 (MQ=255)                                                                                           ccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCa                                      >  7:320113/1‑145 (MQ=255)                                                                                             ggCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAg                                  >  6:204968/1‑147 (MQ=255)                                                                                               cAGTGGCAGCTCACGCGCACAAAGCGGGGCGCGGTGCGC‑‑GCGCTTTGCGCTACTCATGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCt                                <  2:262412/147‑1 (MQ=255)                                                                                                     cAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATgc                          >  3:4636/1‑147 (MQ=255)                                                                                                          cAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTgg                     >  7:254745/1‑147 (MQ=255)                                                                                                                cAGAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATc               >  2:30035/1‑147 (MQ=255)                                                                                                                  gAAAGAGGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATcgc             >  3:216746/1‑147 (MQ=255)                                                                                                                     agagGGGAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATcgccg           <  8:320113/146‑1 (MQ=255)                                                                                                                        ggggAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTgg       >  7:269910/1‑147 (MQ=255)                                                                                                                          ggAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTg                      <  7:186012/130‑1 (MQ=255)                                                                                                                          ggAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTg                      >  8:186012/1‑130 (MQ=255)                                                                                                                          ggAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCg     >  1:67916/1‑147 (MQ=255)                                                                                                                           gAGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCgg    >  2:142903/1‑147 (MQ=255)                                                                                                                            aGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGt   >  6:128462/1‑147 (MQ=255)                                                                                                                            aGCGCTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGt   >  5:294806/1‑147 (MQ=255)                                                                                                                             gcgcTGCGC‑‑GCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTg  <  1:30035/147‑1 (MQ=255)                                                                                                                                              |                                                                                                                                    GGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGC‑‑GCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTG  >  NC_002947/3951022‑3951292

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: ‑