Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,951,161	A→T	100%	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	100.0%	102.6 / NA	32	intergenic (‑125/+70)	PP_3486/PP_3487	cytochrome c/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (21/11);  total (21/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGC  >  NC_002947/3951040‑3951301                                                                                                                          |                                                                                                                                              aaGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAg                                                                                                                                   <  6:289286/134‑1 (MQ=255) aaGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAg                                                                                                                                   >  5:289286/1‑134 (MQ=255)                                     aGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGGTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCa                                                                               >  5:201650/1‑149 (MQ=255)                                      gcgcCCTTGCGCCGCCAACGGGCGGCCCAGCAGCCCCGCCAGGGGCCGCTCAACCGCACAACCAGGGCAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCAt                                                                              <  6:201650/149‑1 (MQ=25)                                               gggccgtaaaGGGCTGCGCACCAGCCCGGGCAGTGGATGATAATGCGCACAAAGAGGTGAGCGCTGCGCGCTCCTTTCGCTACGAAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCac                                                                     <  6:292017/142‑1 (MQ=255)                                                 tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑c                                                                                                  >  6:163873/1‑118 (MQ=255)                                                 tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑c                                                                                                  <  5:163873/118‑1 (MQ=255)                                                 tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCACATCCACAGGCGGCCCATGATACTCacc                                                                    >  8:97396/1‑148 (MQ=39)                                                 tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCacc                                                                    >  8:30850/1‑148 (MQ=255)                                                     gAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCaccgaccg                                                               >  5:41860/1‑149 (MQ=255)                                                      aaaGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCgg                                                              >  2:107123/1‑149 (MQ=255)                                                        ggggCTGCTGCGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGcc                                                            >  2:302253/2‑149 (MQ=39)                                                           gCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGc                                                         >  8:368109/1‑149 (MQ=255)                                                             tGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCgg                                                       >  3:63274/1‑149 (MQ=255)                                                                gcagcaGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTg                                                    >  7:135223/1‑149 (MQ=255)                                                                   gcagcCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGt                                                 >  5:107858/1‑149 (MQ=255)                                                                      gcCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCaa                                              >  7:109525/1‑149 (MQ=255)                                                                       ccccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCca                                                                                                          >  8:39367/1‑89 (MQ=255)                                                                       ccccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCca                                                                                                          <  7:39367/89‑1 (MQ=255)                                                                        cccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAAc                                             <  1:107123/149‑1 (MQ=255)                                                                         ccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAg                                           >  1:69110/1‑149 (MQ=255)                                                                         ccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAg                                           >  5:150589/1‑149 (MQ=255)                                                                               gTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTgg                                                   >  3:407247/1‑135 (MQ=255)                                                                               gTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTgg                                                   <  4:407247/135‑1 (MQ=255)                                                                               gTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCAt                                     <  4:63274/149‑1 (MQ=255)                                                                                     gCTCAAGCGCAGAAAGAGGTGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTg                               >  4:114817/1‑149 (MQ=255)                                                                                      cTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTgg                              <  6:107858/149‑1 (MQ=255)                                                                                                 aaaGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCg                                                        <  7:138702/112‑1 (MQ=255)                                                                                                 aaaGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCg                                                        >  8:138702/1‑112 (MQ=255)                                                                                                       gggAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCgg             >  6:306717/1‑149 (MQ=255)                                                                                                               tGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCg     >  5:420170/1‑149 (MQ=255)                                                                                                                  gcgcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGc  <  1:302253/149‑1 (MQ=255)                                                                                                                          |                                                                                                                                              AAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGG‑CCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGC  >  NC_002947/3951040‑3951301

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑