Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,884,962	T→G	14.3%	E139A (GAA→GCA) ‡	yedI ←	inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,884,962	0	T	G	14.3%	109.3 / 10.1	42	E139A (GAA→GCA) ‡	yedI	inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (18/18);  new base G (2/4);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 6.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

CAATGGTCATCACCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAGCACAGGAACGCGCCACCCAGCATC  >  NC_002947/4884819‑4885105                                                                                                                                                 |                                                                                                                                                cAATGGTCATCACCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCTATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCaaaa                                                                                                                                            <  5:357855/149‑1 (MQ=255) cAATGGTCATCACCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCaaaa                                                                                                                                            <  5:135241/149‑1 (MQ=255)      gTCATCACCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTGAAAAAGccaa                                                                                                                                       <  3:178318/149‑2 (MQ=255)       tcatcaCCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACGTATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCATTGATCTTGGATTTTTCAAAAGcca                                                                                                                                        >  1:278737/1‑148 (MQ=255)       tcatcaCCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGccac                                                                                                                                       >  7:87934/1‑148 (MQ=255)         atcaCCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTGAAAAAGccaaga                                                                                                                                     <  6:130303/148‑4 (MQ=255)          tcaCCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAgg                                                                                                                                   <  5:204631/149‑1 (MQ=255)            accaccGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGt                                                                                                                                  <  8:87934/148‑1 (MQ=255)              caccGCAATGCCGGAAAGCACGATGATCTGCTGGGTCTGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCaa                                                                                                                               <  3:282951/149‑1 (MQ=255)              caccGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCaaaa                                                                                                                                            >  3:138996/1‑136 (MQ=255)              caccGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCaaaa                                                                                                                                            <  4:138996/136‑1 (MQ=255)              caccGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTc                                                                                                                                 <  2:313801/147‑1 (MQ=255)              caccGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTc                                                                                                                                 >  1:313801/1‑147 (MQ=255)                                          tgctgGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGAGGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTgcg                                                                                                   >  4:188346/1‑149 (MQ=255)                                                gTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTc                                                                                             >  1:340966/1‑149 (MQ=255)                                                gTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTc                                                                                             >  3:168814/1‑149 (MQ=255)                                                   aGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGt                                                                                           <  1:312896/148‑1 (MQ=255)                                                               gCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATc                                                                              <  3:188346/149‑1 (MQ=255)                                                                   cG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGcctc                                                                                                         >  3:316367/1‑118 (MQ=255)                                                                   cG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGcctc                                                                                                         <  4:316367/118‑1 (MQ=255)                                                                                       gatgatTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTc                                                                                 >  4:43527/1‑123 (MQ=255)                                                                                       gatgatTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAg                                                           <  3:240363/145‑1 (MQ=255)                                                                                       gatgatTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTAATCCTCTTCCTTGCTGTGCAAg                                                           >  4:240363/1‑145 (MQ=255)                                                                                        atgatTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACtt                                                      >  3:231710/1‑149 (MQ=255)                                                                                         tgatTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTc                                                                                 <  6:291245/121‑1 (MQ=255)                                                                                                  ccGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGc                                            <  4:168814/149‑1 (MQ=255)                                                                                                     aCAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTtc                                         <  4:231710/149‑1 (MQ=255)                                                                                                         gATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCtt                                                                     <  6:223639/117‑1 (MQ=255)                                                                                                         gATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCtt                                                                     >  5:223639/1‑117 (MQ=255)                                                                                                            gAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGaaa                                   <  2:340966/148‑1 (MQ=255)                                                                                                              aGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAAccc                                >  3:90207/1‑149 (MQ=255)                                                                                                               gTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCACCGGCCTCCTTGCGCGCGTCGTGCTGTGCCTCCTCCTCTTGCTTGCTGTGCAAGATCTTGTGCGCCAGCTTCTCGACACCCt                               >  8:266995/1‑149 (MQ=255)                                                                                                               gTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCt                               >  7:190493/1‑149 (MQ=255)                                                                                                                      cGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAGc                         <  4:90207/148‑1 (MQ=255)                                                                                                                         aCCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAGCACAg                     >  2:47243/1‑149 (MQ=255)                                                                                                                         aCCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAGCACAg                     >  7:280203/1‑149 (MQ=255)                                                                                                                                      tggtGGCTTTTGAAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAg                          <  2:290401/128‑1 (MQ=255)                                                                                                                                      tggtGGCTTTTGAAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAg                          >  1:290401/4‑131 (MQ=255)                                                                                                                                        ttGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTtctc                                       >  2:145666/1‑116 (MQ=255)                                                                                                                                        ttGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTtctc                                       <  1:145666/116‑1 (MQ=255)                                                                                                                                        gtGGCTTTTGAAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGaa                           <  5:85511/127‑1 (MQ=255)                                                                                                                                        gtGGCTTTTGAAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGaa                           >  6:85511/2‑128 (MQ=255)                                                                                                                                             tttttCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAGCACAGGAACGCGCCACCCAGCATc  >  3:90499/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                CAATGGTCATCACCACCGCAATGCCGGAAAGCACGATGATCTGCTGGGTCAGCGGCGAGTCAGCCACG‑ATACCCAAGGTAATGGCGATGATTTCTGCCGACAGGATGAAGTCGGTACGCACCGCCCCCTTGATCTTGGCTTTTTCAAAAGCCACCAGGTCAACACTGGCATCGGCAACGGCCTCCTTGCGCGCCTCGTGCTGTGCCTCATCCTCTTCCTTGCTGTGCAAGAACTTGTGCGCCAGCTTCTCGAAACCCTCGAAGCACAGGAACGCGCCACCCAGCATC  >  NC_002947/4884819‑4885105

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: ‑