Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,403,756	C→A	8.3%	R94M (AGG→ATG) ‡	PP_3883 ←	holin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,403,756	0	C	A	8.3%	136.0 / 2.1	44	R94M (AGG→ATG) ‡	PP_3883	holin
Reads supporting (aligned to +/- strand):  ref base C (18/22);  new base A (2/2);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

GTTTTGCGCACGGAGGGGGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAATGTGATCGACGA  >  NC_002947/4403615‑4403903                                                                                                                                              |                                                                                                                                                    gTTTTGCGCACGGAGGGGGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGc                                                                                                                                               >  2:197572/1‑148 (MQ=255)     tGCGCACGGAGGGGGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACg                                                                                                                                          >  1:112850/1‑149 (MQ=255)      gcgcACGGAGGGGGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCAGGCCGCtggac                                                                                                                                          <  3:12383/148‑5 (MQ=255)          aCGGAGGGGGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGc                                                                                                                                      >  8:163222/1‑148 (MQ=255)             gAGGGCGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAAcc                                                                                                                                  <  8:80181/149‑1 (MQ=255)                                     gTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGGAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCa                                                                                                           <  4:108750/148‑1 (MQ=255)                                         ccGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGgcg                                                                                                       <  8:226756/148‑1 (MQ=255)                                           gAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCgctg                                                                                                    >  5:188328/1‑149 (MQ=255)                                            aaaaaaCATTTTCACCCCCCTACCCATATTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCgctgc                                                                                                   <  7:139113/149‑1 (MQ=255)                                               aaaCATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTg                                                                                                <  1:197572/149‑1 (MQ=255)                                                 aCATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTtctc                                                                                                             <  6:242519/134‑1 (MQ=255)                                                 aCATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTtctc                                                                                                             >  5:242519/1‑134 (MQ=255)                                                 aCATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTg                                                                                                >  6:270773/1‑147 (MQ=255)                                                 aCATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAAGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTa                                                                                              <  3:52843/149‑1 (MQ=255)                                                   aTTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCATGACTTCTCCAGGCGCTGCTTGTAg                                                                                             >  6:302571/1‑148 (MQ=255)                                                             cccTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGcc                                                                                  >  5:25342/1‑148 (MQ=255)                                                             cccTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCAAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTtttgt                                                                                    >  5:20362/1‑146 (MQ=255)                                                              ccTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAg                                                                                 >  6:199056/1‑149 (MQ=255)                                                                  cccATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGGGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTgg                                                                             <  5:258003/149‑1 (MQ=255)                                                                   ccATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGt                                                                            <  4:162610/149‑1 (MQ=255)                                                                   ccATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGt                                                                            <  8:156117/149‑1 (MQ=255)                                                                     aTTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGc                                                                          <  8:279731/149‑1 (MQ=255)                                                                     aTTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGc                                                                          <  5:302571/149‑1 (MQ=255)                                                                          cATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAg                                                                      <  6:188328/148‑1 (MQ=255)                                                                            tGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGa                                                                   >  7:167234/1‑149 (MQ=255)                                                                              gggCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTtgt                                                                                      <  3:268458/128‑1 (MQ=255)                                                                              gggCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTtgt                                                                                      >  4:268458/1‑128 (MQ=255)                                                                                gCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGc                                                               <  5:270773/149‑1 (MQ=255)                                                                                   ccGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAg                                                            >  8:164111/1‑149 (MQ=255)                                                                                      cAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTg                                                         <  5:199056/149‑1 (MQ=255)                                                                                            ccGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGa                                                   <  8:301875/149‑1 (MQ=255)                                                                                               gAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGcc                                                <  7:164111/149‑1 (MQ=255)                                                                                                    tttCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGaa                                           >  5:262319/1‑149 (MQ=255)                                                                                                               ccTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGCCTGCCAGTTGGTCCGAGCCCAGAACAGAGCCATGt                                >  6:123299/1‑149 (MQ=255)                                                                                                               ccTAATCCAGTGGTGACGTGGGTCCAGCTGCCTGCCGATAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCACGCGCTGCTTGTAGGAGTTGTGGCAGTTCGTGcaca                                                                       <  7:178648/110‑1 (MQ=255)                                                                                                                     ccAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTcc                                                     <  4:89168/122‑1 (MQ=255)                                                                                                                      cAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCcgcg                         >  6:233497/1‑149 (MQ=255)                                                                                                                            tgCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCgg                   >  2:107513/1‑149 (MQ=255)                                                                                                                                gggggTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGa               <  2:112850/149‑1 (MQ=255)                                                                                                                                  gacgttaGCGGCAGGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAAt             >  7:213306/7‑149 (MQ=255)                                                                                                                                   acgttaGCGGCAGGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTc                                    <  3:99577/120‑1 (MQ=255)                                                                                                                                   acgttaGCGGCAGGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTc                                    >  4:99577/6‑125 (MQ=255)                                                                                                                                        aGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAATGTGATc       >  3:243750/1‑149 (MQ=255)                                                                                                                                         gCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAATGTGATcg      <  5:233497/149‑1 (MQ=255)                                                                                                                                             ccTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGAACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAATGTGATcgacga  >  5:283868/1‑149 (MQ=255)                                                                                                                                              cTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGATTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAATGTGATcgacga  >  7:233084/1‑148 (MQ=255)                                                                                                                                              cTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACaga                                       <  7:76660/111‑1 (MQ=255)                                                                                                                                              cTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACaga                                       >  8:76660/1‑111 (MQ=255)                                                                                                                                              |                                                                                                                                                    GTTTTGCGCACGGAGGGGGGCGATCGGTCAGGGATCGTTTCCGAAAAAACATTTTCACCCCCCTACCCATTTTCATGGGGCCCCGCAGCGCCCGGAGGCTTTCAGGAGGGCCTATTCCAGTGGTGCCGGGGGTCCAGCGGCCTGCCGCTAACGTCGCAACCAGCCTCGCGCCCTGACTTCTCCAGGCGCTGCTTGTAGGAGTTGTGGCAGTTGGTGCACAGCGACTGCCAGTTGGTCCGAGCCCAGAACAGAGTCATGTCGCCGCGGTGCGGCTGAATGTGATCGACGA  >  NC_002947/4403615‑4403903

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: ‑