Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,850,064	G→A	9.1%	G610D (GGC→GAC)	PP_3397 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,850,064	0	G	A	9.1%	118.0 / 2.7	44	G610D (GGC→GAC)	PP_3397	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (16/24);  new base A (2/2);  total (18/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

CTAACCAGGCACCGACTGCCAACCCGGAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCACCCCAAGTACGGTCA  >  NC_002947/3849920‑3850192                                                                                                                                                 |                                                                                                                                 cTAACCAGGCACCGACTGCCAACCCGGAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACg                                                                                                                              >  7:131918/1‑149 (MQ=255)         gCACCGACTGCCAACCCGGAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCAc                                                                                                                      <  1:340468/149‑1 (MQ=255)                     aaCCCGGAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAATGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCAc                                                                                                                               >  5:330889/1‑128 (MQ=255)                     aaCCCGGAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAATGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCAc                                                                                                                               <  6:330889/128‑1 (MQ=255)                           gAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGcac                                                                                                             >  4:315347/1‑140 (MQ=255)                           gAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGcac                                                                                                             <  3:315347/140‑1 (MQ=255)                           gAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGAc                                                                                                    <  7:287467/149‑1 (MQ=255)                           gAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGAc                                                                                                    <  4:107764/149‑1 (MQ=255)                           gAAACCGTCGCCACCTTGGGCGGGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGAc                                                                                                    <  4:187626/149‑1 (MQ=255)                           gAAACCGTCGCCACCGTGTGCGTGCCATTGACCATCAACGTGCTGGCCAACGAAACCGATCGAGATGGCAACGTACCGCTGAGCGTGGCCAACATCACCCTGCCGTCCGCCGGCCGTGGCACGGTCAGCACCGTCGGCACAACCGTGAc                                                                                                    <  6:21317/149‑1 (MQ=255)                                 gTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATAc                                                                                              <  1:249505/149‑1 (MQ=255)                                 gTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATAc                                                                                              <  1:19868/149‑1 (MQ=255)                                       aCCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCAcc                                                                                        >  5:36143/1‑149 (MQ=255)                                             ggCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCAc                                                                                  <  5:873/149‑1 (MQ=255)                                                   ccATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAAc                                                                            <  2:337331/149‑1 (MQ=255)                                                     aTTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACg                                                                                                                              >  3:14284/1‑97 (MQ=255)                                                     aTTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACg                                                                                                                              <  4:14284/97‑1 (MQ=255)                                                         aCCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGc                                                                      >  5:284908/1‑149 (MQ=255)                                                         aCCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGc                                                                      <  4:32273/149‑1 (MQ=255)                                                              cAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAAc                                                                            >  1:213969/1‑138 (MQ=255)                                                              cAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAAc                                                                            <  2:213969/138‑1 (MQ=255)                                                               aaCGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTcac                                                                <  6:284908/149‑1 (MQ=255)                                                                        gCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAAc                                                                            <  2:98901/128‑1 (MQ=255)                                                                           aaCGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCAc                                                    <  6:36143/149‑1 (MQ=255)                                                                                cacCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTcac                                                                >  5:100070/1‑132 (MQ=255)                                                                                cacCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTcac                                                                <  6:100070/132‑1 (MQ=255)                                                                                   cGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCtt                                                       <  4:266274/138‑1 (MQ=255)                                                                                   cGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCtt                                                       >  3:266274/1‑138 (MQ=255)                                                                                   cGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGACACGGTCAGCACCGACGGCACAACCGTGACCTATAccc                                                                                            <  5:176376/101‑1 (MQ=255)                                                                                   cGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGACACGGTCAGCACCGACGGCACAACCGTGACCTATAccc                                                                                            >  6:176376/1‑101 (MQ=255)                                                                                    gATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTcacca                                                              >  6:56428/1‑130 (MQ=255)                                                                                                aaCGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGc                                                                                                               >  4:136397/1‑69 (MQ=255)                                                                                                aaCGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGc                                                                                                               <  3:136397/69‑1 (MQ=255)                                                                                                                 ggCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCt                      >  4:139990/1‑141 (MQ=255)                                                                                                                 ggCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCt                      <  3:139990/141‑1 (MQ=255)                                                                                                                    cAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCAcccc             >  7:243007/1‑147 (MQ=255)                                                                                                                         tCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCACCCCAAGTACg      <  8:243007/149‑1 (MQ=255)                                                                                                                          cACCCAGCCGGCCGCCGGCCGTGACACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCt                      >  7:307504/1‑132 (MQ=255)                                                                                                                          cACCCAGCCGGCCGCCGGCCGTGACACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCt                      <  8:307504/132‑1 (MQ=255)                                                                                                                           aCCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCACCCCAAGt         <  7:243298/144‑1 (MQ=255)                                                                                                                           aCCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCACCCCAAGt         >  8:243298/1‑144 (MQ=255)                                                                                                                             ccAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCACCCCAAGTACGGTCa  >  1:313868/1‑149 (MQ=255)                                                                                                                                  cggccgccggccgTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTc                   >  5:43167/1‑127 (MQ=255)                                                                                                                                  cggccgccggccgTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTc                   <  6:43167/127‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                 CTAACCAGGCACCGACTGCCAACCCGGAAACCGTCGCCACCTTGGGCGTGCCATTGACCATCAACGTGCTGGCCAACGACACCGATCCAGAAGGCAACGTACCGCTGAGCGTGGCCAACATCACCCAGCCGGCCGCCGGCCGTGGCACGGTCAGCACCGACGGCACAACCGTGACCTATACCCCACCGGCCACTGTAACCACAGCCTTCACCACCACCTTCACCTACCAGGCACGTGACTCACTGGGGGGTCTGTCCACCCCAAGTACGGTCA  >  NC_002947/3849920‑3850192

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑