Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,842,904:1	+G	20.9%	intergenic (+48/‑249)	ccoP‑II → / → PP_4259	cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,842,904	1	.	G	20.9%	109.7 / 37.0	43	intergenic (+48/‑249)	ccoP‑II/PP_4259	cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
Reads supporting (aligned to +/- strand):  ref base . (18/16);  new base G (2/7);  total (20/23)
Fisher's exact test for biased strand distribution p-value = 1.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.00e-01

CCGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCATACTGC  >  NC_002947/4842758‑4843050                                                                                                                                                     |                                                                                                                                                   ccGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCt‑t                                                                                                                                                   <  2:130764/148‑1 (MQ=255)   ggCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCtgtg                                                                                                                                                  >  1:62615/1‑144 (MQ=255)    gCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAg                                                                                                                                               <  2:192505/149‑1 (MQ=255)       cAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCATACGTCTACACCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGCGTAAACCCGCTCCTAAAAAGGATCCT‑Tga                                                                                                                                                 >  3:59315/1‑143 (MQ=255)          gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGCgg                                                                                                                                         <  6:80650/149‑1 (MQ=255)          gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCCGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGCgg                                                                                                                                         <  1:245514/149‑1 (MQ=255)          gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCCGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCCGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTCGGAGCgg                                                                                                                                         <  7:247605/149‑1 (MQ=38)           aacaacTGCATGGCAACGAAAATGTGCACTTGCTGGGGGCTTACGTCTACATCCTTGCCCACCATGCTGAGCCGGCCAAGGCTGAGTTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCgg                                                                                                                                         <  1:282957/149‑1 (MQ=37)           aacaacTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGCggg                                                                                                                                        <  2:62615/149‑1 (MQ=255)                   cAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCgg                                                                                                                                         <  4:55499/140‑1 (MQ=255)                   cAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCgg                                                                                                                                         >  3:55499/1‑140 (MQ=255)                   cAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTAcc                                                                                                                                  <  3:144552/147‑1 (MQ=255)                               aaGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCgg                                                                                                                    >  2:42842/1‑149 (MQ=255)                                          gCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAg                                                                                                         >  6:144879/1‑149 (MQ=255)                                                      cGTCTACAGCCTGTCGCACCAGGCTGCGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCa                                                                                              <  5:100775/148‑1 (MQ=255)                                                       gTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAgg                                                                                            >  6:327775/1‑149 (MQ=255)                                                           tcAGCCTGGTGCGACAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCAAAACAGGATGCA‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGGACAGCATTTATCGGAGGCAAg                                                                                        >  8:39756/2‑149 (MQ=25)                                                           tcAGCCTGGTGCGACAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCACCGACACAGGCTCCG‑TGTATGAGCGGGTTTAACCGCGAAGAGGCCGGTACTGGCACCGCCTTTCTCGCAGGCAAg                                                                                        >  8:148676/2‑149 (MQ=37)                                                            cAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCaa                                                                                         <  5:144879/147‑1 (MQ=255)                                                                   tCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCt                                                                                  <  5:327775/147‑1 (MQ=255)                                                                     gCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAACCCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGa                                                                               <  8:171398/148‑1 (MQ=255)                                                                          aGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCTGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAtt                                                                         <  5:184531/149‑1 (MQ=255)                                                                                    ggCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAgg                                                                                                                                              >  3:43624/1‑70 (MQ=17)                                                                                    ggCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAgg                                                                                                                                              <  4:43624/70‑1 (MQ=17)                                                                                                g‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGTAGCGGTTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGttt                                                    <  7:39756/148‑1 (MQ=255)                                                                                                       caggcCTGGCCTCTTGGGGGGAAAACCCGCTCCTACACAGGAGCCT‑TGTAGCAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCa                                             <  7:148676/149‑1 (MQ=38)                                                                                                              ggcctCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGGTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTGTCGCAGGGAAGTGACCGGGATCAATTGACACCCGCCATCACACGTTTCATACCACGAAcc                                       >  6:321337/1‑148 (MQ=37)                                                                                                               gcctCTTCGCGGGTTAACCCGCTGCGTCACAGGATGCG‑TGTAGGAGCGGGTTTACCCGCGGAGAGGCCGGTACGGGCACAGGATTTATCGCAGGGAAGTGGCCGGGATGGATTGCAACCCGCCATAACACGTTTCCTACCACGCAccc                                      >  6:316568/1‑148 (MQ=19)                                                                                                                 ctctTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAAc                                   <  1:42842/149‑1 (MQ=255)                                                                                                                          ggTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATAcc                                              >  3:43239/1‑129 (MQ=255)                                                                                                                          ggTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATAcc                                              <  4:43239/129‑1 (MQ=255)                                                                                                                                 ccGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCg                     >  4:99287/1‑147 (MQ=255)                                                                                                                                 ccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGttt                                                    >  3:256220/1‑116 (MQ=25)                                                                                                                                 ccGCTCCTACA‑AGGATCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGttt                                                    <  4:256220/116‑1 (MQ=25)                                                                                                                                     tCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGc               >  8:339803/1‑149 (MQ=255)                                                                                                                                          cacaGGATCCT‑TGTAGGAGCTGGTTTACCCGCGAAGAGTACGGTACTGGCACAGCATTTCTCGCATGCAAGTGAACTGGATCAATTGACACAAGCCATAACACCTTTAATACCACGAACCCAACGCGACTAAAGGTCTCAGTGCGAAcc          >  4:270635/1‑149 (MQ=255)                                                                                                                                          cacaGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGaa            <  7:339803/147‑1 (MQ=255)                                                                                                                                           acaGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAt                                                                          <  8:183238/84‑1 (MQ=255)                                                                                                                                           acaGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAAcc          >  6:112902/1‑148 (MQ=255)                                                                                                                                             aGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGtt                                                     >  2:96053/1‑103 (MQ=255)                                                                                                                                             aGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGtt                                                     <  1:96053/103‑1 (MQ=255)                                                                                                                                             aGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAg                         >  2:95065/1‑131 (MQ=255)                                                                                                                                             aGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAg                         <  1:95065/131‑1 (MQ=255)                                                                                                                                             aGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCa        >  1:94020/1‑148 (MQ=255)                                                                                                                                                  ccT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCATACTGc  >  5:102119/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CCGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAG‑TAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGCGAACCCATACTGC  >  NC_002947/4842758‑4843050

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: ‑